3UWV

Crystal structure of Staphylococcus Aureus triosephosphate isomerase complexed with 2-phosphoglyceric acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M9Y	PDB ENTRY 3M9Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	1.6M TRISODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.953	α = 90
b = 78.953	β = 90
c = 175.124	γ = 90

Symmetry
Space Group	P 43 21 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	IMAGE PLATE	RIGAKU RAXIS IV++	MIRROR	2010-12-10	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	2.07	71.976	99.3	0.082	22.1	13.7		34450			26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.18	96.9		0.454	0.454	1.7	11.4

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	PDB ENTRY 3M9Y	2.07	20	32582	1727	99.2	0.187	0.185	0.222	RANDOM	34.44

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]
1.48			1.48		-2.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.353
r_dihedral_angle_3_deg	12.827
r_dihedral_angle_4_deg	9.079
r_dihedral_angle_1_deg	4.979
r_scangle_it	4.79
r_scbond_it	2.765
r_angle_refined_deg	1.125
r_mcangle_it	1.015
r_mcbond_it	0.516
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.353
r_dihedral_angle_3_deg	12.827
r_dihedral_angle_4_deg	9.079
r_dihedral_angle_1_deg	4.979
r_scangle_it	4.79
r_scbond_it	2.765
r_angle_refined_deg	1.125
r_mcangle_it	1.015
r_mcbond_it	0.516
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3840
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	25

Software

Software
Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement
XDS	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.