X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VQG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2810.95 M ammonium sulfate, 50 mM sodium acetate, pH 5.5 and 5% glucose.
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.03α = 90
b = 66.03β = 90
c = 224.48γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2015-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.439.6192.80.0778.73.718600
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)
12.42.51950.5351.636867

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 REPLACEMENTTHROUGHOUT5VQG2.439.611769387891.10.1980.1950.262RANDOM45.17
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]
-0.36-0.360.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.697
r_dihedral_angle_4_deg20.02
r_dihedral_angle_3_deg15.052
r_long_range_B_refined8.179
r_long_range_B_other8.177
r_dihedral_angle_1_deg6.949
r_scangle_other5.839
r_mcangle_it4.773
r_mcangle_other4.772
r_scbond_it3.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.697
r_dihedral_angle_4_deg20.02
r_dihedral_angle_3_deg15.052
r_long_range_B_refined8.179
r_long_range_B_other8.177
r_dihedral_angle_1_deg6.949
r_scangle_other5.839
r_mcangle_it4.773
r_mcangle_other4.772
r_scbond_it3.611
r_scbond_other3.603
r_mcbond_it3.108
r_mcbond_other3.106
r_angle_refined_deg1.482
r_angle_other_deg0.774
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms3213
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing