X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R61 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.229335% 2-ethoxyethanol, 0.1 M Na/K phosphate buffer pH 6.2, 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.3146.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.21α = 90
b = 70.198β = 105.77
c = 104.839γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2022-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

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
12.5344.9197.30.1010.1210.0660.9528.23.341332
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)
12.532.6399.90.5490.6490.3430.7452.23.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5343.4539259206597.340.25280.25030.2987RANDOM57.175
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]
-0.080.090.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.328
r_dihedral_angle_3_deg24.504
r_dihedral_angle_4_deg19.619
r_long_range_B_refined10.846
r_long_range_B_other10.829
r_dihedral_angle_1_deg6.836
r_scangle_other5.286
r_mcangle_other5.134
r_mcangle_it5.133
r_scbond_it3.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.328
r_dihedral_angle_3_deg24.504
r_dihedral_angle_4_deg19.619
r_long_range_B_refined10.846
r_long_range_B_other10.829
r_dihedral_angle_1_deg6.836
r_scangle_other5.286
r_mcangle_other5.134
r_mcangle_it5.133
r_scbond_it3.168
r_scbond_other3.168
r_mcbond_it3.162
r_mcbond_other3.157
r_angle_refined_deg1.492
r_angle_other_deg1.249
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9573
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing