X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2940.4 M Ammonium phosphate
Crystal Properties
Matthews coefficientSolvent content
1.831.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.747α = 90
b = 58.815β = 90
c = 88.568γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-18MSINGLE 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
11.647.7899.90.053125.8812.9239917
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)
11.61.799.40.830.912.89

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 REPLACEMENTTHROUGHOUT4V2Y1.647.7837914200399.860.195060.193780.21917RANDOM32.291
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]
-0.120.77-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.532
r_dihedral_angle_4_deg12.173
r_dihedral_angle_3_deg11.565
r_dihedral_angle_1_deg6.154
r_long_range_B_refined5.471
r_long_range_B_other5.415
r_scangle_other2.564
r_mcangle_it1.903
r_mcangle_other1.902
r_scbond_it1.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.532
r_dihedral_angle_4_deg12.173
r_dihedral_angle_3_deg11.565
r_dihedral_angle_1_deg6.154
r_long_range_B_refined5.471
r_long_range_B_other5.415
r_scangle_other2.564
r_mcangle_it1.903
r_mcangle_other1.902
r_scbond_it1.634
r_scbond_other1.624
r_angle_refined_deg1.613
r_mcbond_it1.179
r_mcbond_other1.177
r_angle_other_deg0.985
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.009
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 Atoms2492
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling