9BS5 | pdb_00009bs5

Bacteroides ovatus GH97C Sus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZQ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Molecular Dimensions Morpheus screen condition that included 100 mM NaHEPES/MOPS pH 7.5 (Thermo), 100 mM amino acids and 36% precipitant mix 4
Crystal Properties
Matthews coefficientSolvent content
2.6954.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.855α = 90
b = 116.528β = 90
c = 144.004γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 300 mm2022-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

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
11.4651.2699.80.10.995.75.8312566
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.4899.80.524

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4651.262966651589999.960.2050.2040.20780.2240.2278RANDOM15.143
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]
-1.21-1.342.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.626
r_dihedral_angle_3_deg11.595
r_dihedral_angle_4_deg9.739
r_dihedral_angle_1_deg7.508
r_long_range_B_refined2.8
r_long_range_B_other2.8
r_rigid_bond_restr2.707
r_angle_refined_deg1.246
r_angle_other_deg1.231
r_scangle_other1.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.626
r_dihedral_angle_3_deg11.595
r_dihedral_angle_4_deg9.739
r_dihedral_angle_1_deg7.508
r_long_range_B_refined2.8
r_long_range_B_other2.8
r_rigid_bond_restr2.707
r_angle_refined_deg1.246
r_angle_other_deg1.231
r_scangle_other1.008
r_mcangle_it0.885
r_mcangle_other0.885
r_scbond_it0.776
r_scbond_other0.776
r_mcbond_it0.628
r_mcbond_other0.628
r_chiral_restr0.056
r_gen_planes_refined0.005
r_bond_refined_d0.004
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11035
Nucleic Acid Atoms
Solvent Atoms1492
Heterogen Atoms157

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
xia2data reduction
PHENIXphasing