2RGO | pdb_00002rgo

Structure of Alpha-Glycerophosphate Oxidase from Streptococcus sp.: A Template for the Mitochondrial Alpha-Glycerophosphate Dehydrogenase

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	PEG 1000, Tris, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.363	α = 90
b = 106.785	β = 99.18
c = 58.887	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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9296	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.4	28.89		0.064	9.9			54822

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.53			0.298	2.8		8692

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 2RGH	2.4	12	54822	2938	94.87	0.23808	0.23808	0.23759	0.23	0.24708	0.27	RANDOM	62.886

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]
0.02		0.04	-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.125
r_dihedral_angle_4_deg	17.634
r_dihedral_angle_3_deg	15.517
r_scangle_it	3.237
r_dihedral_angle_1_deg	3.101
r_mcangle_it	2.539
r_scbond_it	2.173
r_angle_refined_deg	1.675
r_mcbond_it	1.457
r_nbtor_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.125
r_dihedral_angle_4_deg	17.634
r_dihedral_angle_3_deg	15.517
r_scangle_it	3.237
r_dihedral_angle_1_deg	3.101
r_mcangle_it	2.539
r_scbond_it	2.173
r_angle_refined_deg	1.675
r_mcbond_it	1.457
r_nbtor_refined	0.328
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.276
r_symmetry_hbond_refined	0.201
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.111
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8524
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	106

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.