X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29420 % PEG 3350, 0.2 M Ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
1.9436.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.728α = 90
b = 59.163β = 105.59
c = 61.751γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.549.17990.080.9989.73.3768423
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5997.50.880.561.153.14

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 REPLACEMENTTHROUGHOUT4v2y1.549.1765001342299.640.159430.15780.19039RANDOM21.669
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]
-0.240.180.32-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.608
r_dihedral_angle_4_deg18.113
r_dihedral_angle_3_deg12.426
r_long_range_B_refined7.246
r_long_range_B_other7.229
r_dihedral_angle_1_deg7.117
r_scangle_other5.264
r_angle_refined_deg4.409
r_mcangle_it3.844
r_mcangle_other3.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.608
r_dihedral_angle_4_deg18.113
r_dihedral_angle_3_deg12.426
r_long_range_B_refined7.246
r_long_range_B_other7.229
r_dihedral_angle_1_deg7.117
r_scangle_other5.264
r_angle_refined_deg4.409
r_mcangle_it3.844
r_mcangle_other3.844
r_scbond_it3.407
r_scbond_other3.406
r_mcbond_it2.641
r_mcbond_other2.635
r_angle_other_deg1.407
r_chiral_restr0.198
r_gen_planes_refined0.043
r_bond_refined_d0.037
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 Atoms3425
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing