2R45

Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with 2-phospho-d-glyceric 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 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.744	α = 90
b = 113.908	β = 90
c = 193.069	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				2007-04-17	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	2.3	50	98.5	0.099	9.8	6.2		55038

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)
	2.3	2.38	88.1		0.505		3.6	4864

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	2.3	10	54271	2754	98.49	0.194	0.19	0.27	RANDOM	38.265

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]
0.76			0.77		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.724
r_dihedral_angle_3_deg	21.924
r_dihedral_angle_4_deg	20.119
r_dihedral_angle_1_deg	10.074
r_scangle_it	4.952
r_scbond_it	3.272
r_angle_refined_deg	2.747
r_mcangle_it	2.143
r_mcbond_it	1.328
r_symmetry_hbond_refined	0.371

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.724
r_dihedral_angle_3_deg	21.924
r_dihedral_angle_4_deg	20.119
r_dihedral_angle_1_deg	10.074
r_scangle_it	4.952
r_scbond_it	3.272
r_angle_refined_deg	2.747
r_mcangle_it	2.143
r_mcbond_it	1.328
r_symmetry_hbond_refined	0.371
r_nbtor_refined	0.322
r_nbd_refined	0.293
r_xyhbond_nbd_refined	0.239
r_chiral_restr	0.206
r_symmetry_vdw_refined	0.201
r_bond_refined_d	0.028
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7924
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	398

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 R01GM157729.