8S71 | pdb_00008s71

Oxidoreductase B from Phytophthora sojae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.1M sodium acetate trihydrate pH 4.5, 2.0M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.067	α = 90
b = 106.897	β = 114.099
c = 44.815	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 4M		2023-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.97	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	53.42	99.4	0.989	6.6	7.3		26881

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	2.05	2.09			0.768

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.05	53.42	21448	1027	99.204	0.171	0.168	0.177	0.2322	0.2328	26.66

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]
0.595		-0.096	-1.553		0.745

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.988
r_dihedral_angle_6_deg	15.725
r_lrange_it	7.196
r_dihedral_angle_1_deg	7.155
r_lrange_other	7.153
r_dihedral_angle_2_deg	6.319
r_scangle_it	5.4
r_scangle_other	5.399
r_mcangle_other	3.45
r_mcangle_it	3.449
r_scbond_it	3.431
r_scbond_other	3.431
r_mcbond_it	2.395
r_mcbond_other	2.378
r_angle_refined_deg	1.436
r_angle_other_deg	0.474
r_symmetry_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.223
r_nbd_other	0.222
r_symmetry_nbd_other	0.205
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.183
r_symmetry_nbtor_other	0.085
r_metal_ion_refined	0.077
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2710
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
TRUNCATE	data scaling
MOLREP	phasing