X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V1SDimer

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2 M Sodium chloride, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.3447.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.49α = 90
b = 82.64β = 98.52
c = 171.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2022-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6726.42999.90.1080.1210.0540.99611.24.969947
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.672.731000.6610.7390.3260.7945

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.6726.42969933345999.8710.1970.19560.2177RANDOM47.873
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.057-1.4310.1850.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.273
r_dihedral_angle_6_deg13.13
r_dihedral_angle_1_deg7.453
r_dihedral_angle_2_deg5.926
r_lrange_it3.735
r_lrange_other3.734
r_scangle_it1.738
r_scangle_other1.738
r_mcangle_it1.629
r_mcangle_other1.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.273
r_dihedral_angle_6_deg13.13
r_dihedral_angle_1_deg7.453
r_dihedral_angle_2_deg5.926
r_lrange_it3.735
r_lrange_other3.734
r_scangle_it1.738
r_scangle_other1.738
r_mcangle_it1.629
r_mcangle_other1.629
r_scbond_it1.032
r_scbond_other1.032
r_angle_refined_deg0.991
r_mcbond_it0.94
r_mcbond_other0.94
r_angle_other_deg0.367
r_symmetry_nbd_refined0.26
r_nbd_other0.243
r_symmetry_xyhbond_nbd_refined0.223
r_xyhbond_nbd_refined0.216
r_nbd_refined0.193
r_symmetry_nbd_other0.19
r_nbtor_refined0.178
r_symmetry_nbtor_other0.08
r_ncsr_local_group_70.076
r_ncsr_local_group_160.073
r_ncsr_local_group_30.072
r_ncsr_local_group_130.072
r_ncsr_local_group_140.07
r_ncsr_local_group_250.07
r_ncsr_local_group_260.07
r_ncsr_local_group_50.069
r_ncsr_local_group_110.068
r_ncsr_local_group_210.068
r_ncsr_local_group_230.068
r_ncsr_local_group_280.068
r_ncsr_local_group_80.067
r_ncsr_local_group_150.067
r_ncsr_local_group_180.067
r_ncsr_local_group_190.067
r_ncsr_local_group_220.066
r_ncsr_local_group_10.065
r_ncsr_local_group_40.063
r_ncsr_local_group_120.063
r_ncsr_local_group_90.061
r_ncsr_local_group_200.061
r_ncsr_local_group_100.059
r_ncsr_local_group_240.059
r_ncsr_local_group_270.059
r_chiral_restr0.057
r_ncsr_local_group_20.056
r_ncsr_local_group_60.049
r_ncsr_local_group_170.049
r_bond_refined_d0.018
r_bond_other_d0.005
r_gen_planes_refined0.005
r_chiral_restr_other0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19065
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing