X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LKU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG 3350, 0.12 mM benzamidine hydrochloride, 200 mM potassium formate
Crystal Properties
Matthews coefficientSolvent content
2.0138.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.326α = 90
b = 53.464β = 102.396
c = 46.081γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2023-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9677ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
1353.8891.50.9926.35.416784
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.220.311

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3.00253.877409719876.3370.1980.19380.275474.837
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]
0.3150.5860.149-0.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.464
r_dihedral_angle_6_deg12.955
r_lrange_it12.481
r_lrange_other12.479
r_dihedral_angle_1_deg8.891
r_scangle_it7.997
r_scangle_other7.953
r_mcangle_it7.854
r_mcangle_other7.851
r_dihedral_angle_2_deg5.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.464
r_dihedral_angle_6_deg12.955
r_lrange_it12.481
r_lrange_other12.479
r_dihedral_angle_1_deg8.891
r_scangle_it7.997
r_scangle_other7.953
r_mcangle_it7.854
r_mcangle_other7.851
r_dihedral_angle_2_deg5.15
r_mcbond_it4.845
r_mcbond_other4.845
r_scbond_it4.742
r_scbond_other4.713
r_angle_refined_deg1.158
r_angle_other_deg0.394
r_nbd_refined0.232
r_symmetry_nbd_other0.208
r_xyhbond_nbd_refined0.196
r_nbtor_refined0.183
r_nbd_other0.178
r_symmetry_nbd_refined0.158
r_symmetry_xyhbond_nbd_refined0.127
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.049
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2311
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing