2Z9U

Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti at 2.0 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VJO	PDB ID 1VJO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.05	277	0.1M HEPES, 2M Ammonium sulfate, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.545	α = 90
b = 68.545	β = 90
c = 311.635	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 V		2006-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	50	97.8	0.084	10.6	5		58804		-3	18.89

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	1.97	97.2		0.379		5.6	5701

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 ID 1VJO	2	15	47892	2551	97.93	0.15809	0.15558	0.20553	RANDOM	18.596

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.224
r_scbond_it	2.106
r_angle_refined_deg	1.44
r_mcangle_it	1.119
r_mcbond_it	0.729
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.203
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.224
r_scbond_it	2.106
r_angle_refined_deg	1.44
r_mcangle_it	1.119
r_mcbond_it	0.729
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.203
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5832
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection

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.