X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1 M BIS-TRIS propane pH 8.5, 0.2 M NaBr, 20% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1242.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.96α = 90
b = 87.17β = 102.26
c = 109.626γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972422ESRFID23-1

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
12.847.7895.960.2493.83.432860
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9484.11.3

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 REPLACEMENTTHROUGHOUT1VFH2.847.7832860169395.960.2110.208470.25918RANDOM44.888
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]
-1.3-15.96-3.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.51
r_dihedral_angle_4_deg17.845
r_dihedral_angle_3_deg15.6
r_long_range_B_other8.398
r_long_range_B_refined8.397
r_dihedral_angle_1_deg6.423
r_scangle_other5.38
r_mcangle_it4.971
r_mcangle_other4.971
r_scbond_it3.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.51
r_dihedral_angle_4_deg17.845
r_dihedral_angle_3_deg15.6
r_long_range_B_other8.398
r_long_range_B_refined8.397
r_dihedral_angle_1_deg6.423
r_scangle_other5.38
r_mcangle_it4.971
r_mcangle_other4.971
r_scbond_it3.29
r_scbond_other3.29
r_mcbond_it3.081
r_mcbond_other3.081
r_angle_refined_deg1.601
r_angle_other_deg1.393
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms11337
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing