8VDW

X-Ray Crystal Structure of the biotin synthase from V. parvula


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOtherunpublished structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52980.1M Bis-Tris pH 5.5, 0.2M NH4OAc, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.465α = 90
b = 70.218β = 90
c = 195.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirrors2018-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9793NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.80729.699.70.0940.1020.0390.99912.66.760902
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.85960.7570.8270.3280.8556.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.80729.655335186593.720.180220.178680.22689RANDOM27.7
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]
3.37-1.25-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.957
r_dihedral_angle_2_deg7.06
r_long_range_B_refined6.623
r_dihedral_angle_1_deg6.589
r_long_range_B_other6.393
r_scangle_other4.945
r_mcangle_it3.327
r_mcangle_other3.327
r_scbond_it3.175
r_scbond_other3.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.957
r_dihedral_angle_2_deg7.06
r_long_range_B_refined6.623
r_dihedral_angle_1_deg6.589
r_long_range_B_other6.393
r_scangle_other4.945
r_mcangle_it3.327
r_mcangle_other3.327
r_scbond_it3.175
r_scbond_other3.175
r_angle_refined_deg2.432
r_mcbond_it2.382
r_mcbond_other2.379
r_angle_other_deg1.095
r_chiral_restr0.196
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms5113
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing