X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YUK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0840.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.305α = 90
b = 41.224β = 104.157
c = 72.047γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.9793PAL/PLS7A (6B, 6C1)

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
11.230.002960.0920.0990.0360.99324.37.672609
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)
11.21.2293.30.6070.6510.2350.843.27.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5YUK1.23072478371096.0190.1220.120.149714.04
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]
-0.037-0.10.0150.064
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.165
r_dihedral_angle_2_deg36.171
r_dihedral_angle_4_deg25.397
r_dihedral_angle_3_deg12.732
r_sphericity_bonded12.699
r_dihedral_angle_1_deg7.111
r_rigid_bond_restr6.152
r_lrange_it4.996
r_lrange_other4.606
r_scangle_other4.306
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.165
r_dihedral_angle_2_deg36.171
r_dihedral_angle_4_deg25.397
r_dihedral_angle_3_deg12.732
r_sphericity_bonded12.699
r_dihedral_angle_1_deg7.111
r_rigid_bond_restr6.152
r_lrange_it4.996
r_lrange_other4.606
r_scangle_other4.306
r_scangle_it4.305
r_scbond_other3.837
r_scbond_it3.833
r_mcangle_other3.227
r_mcangle_it3.191
r_angle_refined_deg2.644
r_mcbond_it2.435
r_mcbond_other2.374
r_angle_other_deg1.344
r_nbd_other0.341
r_symmetry_nbd_refined0.312
r_nbd_refined0.287
r_chiral_restr0.236
r_symmetry_xyhbond_nbd_refined0.223
r_symmetry_nbd_other0.194
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.138
r_symmetry_nbtor_other0.091
r_symmetry_xyhbond_nbd_other0.062
r_bond_refined_d0.031
r_gen_planes_refined0.015
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing