X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZYVPDB ENTRY 3ZYV

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4650.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.93α = 90
b = 148.93β = 90
c = 133.25γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.674.461000.2611.216.5466001.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.691001.181.515.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZYV2.6105.3144241235999.970.190990.188750.233RANDOM75.477
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]
0.110.11-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.827
r_dihedral_angle_4_deg15.574
r_dihedral_angle_3_deg14.142
r_dihedral_angle_1_deg6.206
r_long_range_B_refined3.713
r_long_range_B_other3.707
r_scangle_other2.009
r_mcangle_it1.957
r_mcangle_other1.957
r_angle_refined_deg1.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.827
r_dihedral_angle_4_deg15.574
r_dihedral_angle_3_deg14.142
r_dihedral_angle_1_deg6.206
r_long_range_B_refined3.713
r_long_range_B_other3.707
r_scangle_other2.009
r_mcangle_it1.957
r_mcangle_other1.957
r_angle_refined_deg1.286
r_scbond_it1.169
r_scbond_other1.169
r_mcbond_it1.122
r_mcbond_other1.122
r_angle_other_deg0.897
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms9988
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing