3LC2

Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin 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 Properties
Matthews coefficient	Solvent content
2.09	41.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.057	α = 90
b = 103.025	β = 109.4
c = 90.303	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 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	2.793	85.178	99.2	0.134		3.8	29489	29489			46

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	2.79	2.94	96.9		0.497	2.7	3.7	4196

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3H48	2.8	20	29373	1492	99.82	0.184	0.181	0.241	RANDOM	37.376

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]
-0.98		-1.33	2.33		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.147
r_dihedral_angle_4_deg	20.644
r_dihedral_angle_3_deg	17.302
r_scangle_it	6.637
r_dihedral_angle_1_deg	6.242
r_scbond_it	3.722
r_angle_refined_deg	1.432
r_mcangle_it	1.31
r_mcbond_it	0.626
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.147
r_dihedral_angle_4_deg	20.644
r_dihedral_angle_3_deg	17.302
r_scangle_it	6.637
r_dihedral_angle_1_deg	6.242
r_scbond_it	3.722
r_angle_refined_deg	1.432
r_mcangle_it	1.31
r_mcbond_it	0.626
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10124
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	61

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.