X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1 M Bis-tris pH 6.5; 20% PEG 5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.39α = 90
b = 100.83β = 97.85
c = 53.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M-F2017-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.752.9297.60.190.160.944.54.14423918
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7495.80.690.610.551.23.4

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 REPLACEMENTTHROUGHOUT2VZ71.750.4242041216797.460.191530.189650.22807RANDOM25.716
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]
-1.180.042.9-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.969
r_dihedral_angle_4_deg14.613
r_dihedral_angle_3_deg12.982
r_dihedral_angle_1_deg5.907
r_long_range_B_refined4.751
r_long_range_B_other4.751
r_scangle_other3.465
r_mcangle_other2.419
r_mcangle_it2.415
r_scbond_it2.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.969
r_dihedral_angle_4_deg14.613
r_dihedral_angle_3_deg12.982
r_dihedral_angle_1_deg5.907
r_long_range_B_refined4.751
r_long_range_B_other4.751
r_scangle_other3.465
r_mcangle_other2.419
r_mcangle_it2.415
r_scbond_it2.347
r_scbond_other2.345
r_mcbond_it1.746
r_mcbond_other1.726
r_angle_refined_deg1.532
r_angle_other_deg0.897
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms3029
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing