X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29850mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1442.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.434α = 90
b = 120.434β = 90
c = 42.227γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNFPSS BEAMLINE BL19U10.979NFPSSBL19U1

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
12.9860.221000.11614.14.94643
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)
133.050.492

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 REPLACEMENTTHROUGHOUT4DVA2.9860.2244152281000.1730.1680.268RANDOM66.14
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]
-3.02-1.51-3.029.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.801
r_dihedral_angle_3_deg16.251
r_dihedral_angle_4_deg16.175
r_long_range_B_refined8.619
r_long_range_B_other8.618
r_dihedral_angle_1_deg7.258
r_scangle_other5.542
r_mcangle_it5.412
r_mcangle_other5.412
r_scbond_it3.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.801
r_dihedral_angle_3_deg16.251
r_dihedral_angle_4_deg16.175
r_long_range_B_refined8.619
r_long_range_B_other8.618
r_dihedral_angle_1_deg7.258
r_scangle_other5.542
r_mcangle_it5.412
r_mcangle_other5.412
r_scbond_it3.381
r_scbond_other3.38
r_mcbond_it3.273
r_mcbond_other3.267
r_angle_refined_deg1.459
r_angle_other_deg0.926
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms1933
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing