8S6S | pdb_00008s6s

Oxidoreductase from Phytophthora sojae

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Z5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.267	α = 90
b = 73.129	β = 90
c = 116.418	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	PIXEL	DECTRIS EIGER X 16M		2023-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.98	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.789	61.925	100	0.998	16.3	13.3		38093

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	1.789	1.82			0.829

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	1.789	61.925	38093	1905	99.974	0.163	0.1608	0.1724	0.2023	0.2072	27.585

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]
0.746			-1.326		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.198
r_dihedral_angle_3_deg	15.028
r_lrange_it	8.645
r_lrange_other	8.637
r_dihedral_angle_1_deg	7.218
r_scangle_it	7.111
r_scangle_other	7.072
r_dihedral_angle_2_deg	4.984
r_scbond_it	4.634
r_scbond_other	4.591
r_mcangle_it	4.144
r_mcangle_other	4.144
r_mcbond_it	2.893
r_mcbond_other	2.893
r_angle_refined_deg	1.56
r_angle_other_deg	0.558
r_nbd_refined	0.218
r_symmetry_nbd_other	0.204
r_xyhbond_nbd_refined	0.203
r_nbtor_refined	0.185
r_nbd_other	0.149
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbd_refined	0.102
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.055
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2686
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
AutoProcess	data reduction
Aimless	data scaling
MOLREP	phasing