9BS5 | pdb_00009bs5

Bacteroides ovatus GH97C Sus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZQ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Molecular 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 coefficient	Solvent content
2.69	54.19

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 300 mm		2022-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.979	APS	21-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.46	51.26	99.8	0.1	0.99	5.7	5.8		312566

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.48	99.8		0.524

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.46	51.26	296665	15899	99.96	0.205	0.204	0.2078	0.224	0.2278	RANDOM	15.143

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			-1.34		2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.626
r_dihedral_angle_3_deg	11.595
r_dihedral_angle_4_deg	9.739
r_dihedral_angle_1_deg	7.508
r_long_range_B_refined	2.8
r_long_range_B_other	2.8
r_rigid_bond_restr	2.707
r_angle_refined_deg	1.246
r_angle_other_deg	1.231
r_scangle_other	1.008
r_mcangle_it	0.885
r_mcangle_other	0.885
r_scbond_it	0.776
r_scbond_other	0.776
r_mcbond_it	0.628
r_mcbond_other	0.628
r_chiral_restr	0.056
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	11035
Nucleic Acid Atoms
Solvent Atoms	1492
Heterogen Atoms	157

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing