X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 3350, serine
Crystal Properties
Matthews coefficientSolvent content
2.244.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.052α = 90
b = 69.866β = 90
c = 87.417γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2015-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.755099.816.96.725375

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 REPLACEMENTTHROUGHOUT1VK11.755024069128099.740.229630.228480.25074RANDOM25.812
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]
-0.7-0.851.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.4
r_dihedral_angle_3_deg11.281
r_dihedral_angle_4_deg8.96
r_dihedral_angle_1_deg6.816
r_long_range_B_refined3.895
r_long_range_B_other3.792
r_angle_refined_deg1.536
r_angle_other_deg0.901
r_mcangle_it0.601
r_mcangle_other0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.4
r_dihedral_angle_3_deg11.281
r_dihedral_angle_4_deg8.96
r_dihedral_angle_1_deg6.816
r_long_range_B_refined3.895
r_long_range_B_other3.792
r_angle_refined_deg1.536
r_angle_other_deg0.901
r_mcangle_it0.601
r_mcangle_other0.6
r_scangle_other0.515
r_mcbond_other0.332
r_mcbond_it0.331
r_scbond_it0.31
r_scbond_other0.31
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
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 Atoms1812
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing