3M9Y | pdb_00003m9y

Crystal structure of Triosephosphate isomerase from methicillin resistant Staphylococcus aureus at 1.9 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BTM	PDB ENTRY 2BTM

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.478	α = 90
b = 79.478	β = 90
c = 175.006	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++	Varimax mirrors	2009-10-10	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 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	1.9	72.365	99.5	0.058	29.5	13.5	44961	44961			24.8

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	1.9	2	97.9		0.433	5.5	12.1	6332

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BTM	1.9	20	44825	2258	99.53	0.161	0.159	0.19	0.205	0.23	RANDOM	31.097

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]
1.1			1.1		-2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.137
r_dihedral_angle_3_deg	13.79
r_dihedral_angle_4_deg	11.336
r_scangle_it	8.335
r_dihedral_angle_1_deg	5.822
r_scbond_it	5.316
r_mcangle_it	2.174
r_angle_refined_deg	1.842
r_mcbond_it	1.275
r_chiral_restr	0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.137
r_dihedral_angle_3_deg	13.79
r_dihedral_angle_4_deg	11.336
r_scangle_it	8.335
r_dihedral_angle_1_deg	5.822
r_scbond_it	5.316
r_mcangle_it	2.174
r_angle_refined_deg	1.842
r_mcbond_it	1.275
r_chiral_restr	0.15
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3825
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	15

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.