3LC7 | pdb_00003lc7

Crystal Structure of apo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicllin resistant Staphylococcus aureus (MRSA252)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M Tris-HCl pH:8.5, 32% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.288	α = 90
b = 94.937	β = 105.73
c = 86.552	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	IMAGE PLATE	RIGAKU RAXIS IV++	Varimax mirrors	2009-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.494	83.311	99.3	0.061	19.1	3.7	34746	34746			38

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)
1	2.49	2.63	96.7		0.281	4.5	3.5	4921

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	3H48	2.5	20	34621	34621	354	99.89	0.188	0.187	0.23	0.249	0.27	RANDOM	40.942

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]
1.66		-0.62	-1.03		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.496
r_dihedral_angle_4_deg	25.01
r_dihedral_angle_3_deg	17.319
r_dihedral_angle_1_deg	7.012
r_scangle_it	6.45
r_scbond_it	3.808
r_angle_refined_deg	1.576
r_mcangle_it	1.441
r_mcbond_it	0.717
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.496
r_dihedral_angle_4_deg	25.01
r_dihedral_angle_3_deg	17.319
r_dihedral_angle_1_deg	7.012
r_scangle_it	6.45
r_scbond_it	3.808
r_angle_refined_deg	1.576
r_mcangle_it	1.441
r_mcbond_it	0.717
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10075
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction
MOLREP	phasing

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.