X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27720% PEG 1000, 0.1M HEPES pH 7, 0.016M Cadmium Chloride, 0.8M Sodium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.713α = 90
b = 105.014β = 90
c = 185.624γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.8246.4599.610.02511.48.738700
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.822.920.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1VQQ2.8246.4536832185699.650.244390.240970.31064RANDOM121.859
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]
0.95-2.351.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.324
r_dihedral_angle_3_deg19.432
r_dihedral_angle_4_deg17.181
r_long_range_B_refined16.82
r_long_range_B_other16.812
r_scangle_other11.896
r_mcangle_it11.893
r_mcangle_other11.892
r_mcbond_it7.715
r_mcbond_other7.707
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.324
r_dihedral_angle_3_deg19.432
r_dihedral_angle_4_deg17.181
r_long_range_B_refined16.82
r_long_range_B_other16.812
r_scangle_other11.896
r_mcangle_it11.893
r_mcangle_other11.892
r_mcbond_it7.715
r_mcbond_other7.707
r_scbond_it7.44
r_scbond_other7.437
r_dihedral_angle_1_deg7.381
r_angle_refined_deg1.133
r_angle_other_deg0.795
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms9900
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing