2R46

Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with 2-phosphopyruvic acid.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.1 M di-Ammonium hydrogen phosphate, 0.1 M Taps, 12% w/v PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.823	α = 90
b = 113.937	β = 90
c = 192.74	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2007-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9803	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	28.89	100	0.099	9.2	9.9		73532

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)
	2.1	2.18	100		0.501			7291

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	10	69138	3671	100	0.193	0.191	0.23	RANDOM	40.577

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]
0.52			0.53		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.382
r_dihedral_angle_3_deg	20.349
r_dihedral_angle_4_deg	16.593
r_dihedral_angle_1_deg	9.302
r_scangle_it	4.444
r_scbond_it	3.028
r_angle_refined_deg	2.512
r_mcangle_it	2.057
r_mcbond_it	1.345
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.382
r_dihedral_angle_3_deg	20.349
r_dihedral_angle_4_deg	16.593
r_dihedral_angle_1_deg	9.302
r_scangle_it	4.444
r_scbond_it	3.028
r_angle_refined_deg	2.512
r_mcangle_it	2.057
r_mcbond_it	1.345
r_nbtor_refined	0.316
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.227
r_symmetry_hbond_refined	0.227
r_symmetry_vdw_refined	0.221
r_chiral_restr	0.208
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7924
Nucleic Acid Atoms
Solvent Atoms	385
Heterogen Atoms	349

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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 R01GM133198.