5OVS

Thiobacillus denitrificans BPH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294100 mM HEPES-NaOH pH 7.0, 600 mM NaF
Crystal Properties
Matthews coefficientSolvent content
2.2545.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.107α = 90
b = 175.23β = 90
c = 205.89γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.339.699.70.1130.99711.75.22127579
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4498.70.8310.7041.985.14

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 DIFFRACTIONSADTHROUGHOUT2.339.55121199637999.720.210340.207980.25523RANDOM42.195
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]
2.940.1-3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.178
r_dihedral_angle_4_deg17.833
r_dihedral_angle_3_deg13.724
r_dihedral_angle_1_deg5.937
r_long_range_B_refined3.931
r_long_range_B_other3.915
r_scangle_other2.095
r_mcangle_it2.033
r_mcangle_other2.032
r_scbond_it1.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.178
r_dihedral_angle_4_deg17.833
r_dihedral_angle_3_deg13.724
r_dihedral_angle_1_deg5.937
r_long_range_B_refined3.931
r_long_range_B_other3.915
r_scangle_other2.095
r_mcangle_it2.033
r_mcangle_other2.032
r_scbond_it1.228
r_scbond_other1.228
r_angle_refined_deg1.188
r_mcbond_it1.185
r_mcbond_other1.185
r_angle_other_deg0.735
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms19861
Nucleic Acid Atoms
Solvent Atoms493
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing