3GK0

Crystal structure of pyridoxal phosphate biosynthetic protein from Burkholderia pseudomallei

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M5W	PDB entry 1M5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	16.4% PEG4000, 0.1 M Hepes NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.33

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 90.09	�� = 118.48
b = 91.864	�� = 116.81
c = 90.024	�� = 93.5

Symmetry
Space Group	P 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	CCD			2008-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97934	APS	24-ID-E

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	2.28	50	96.5	0.107	12.627	3.7		91137

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	2.28	2.38	85.2		0.481	2.1	3	8058

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 1M5W	2.28	46.5	91104	4580	94.2	0.189	0.186	0.245	RANDOM	28.325

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]
-0.58	0.93	-0.84	0.49	-0.65	-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.406
r_dihedral_angle_4_deg	19.242
r_dihedral_angle_3_deg	15.597
r_dihedral_angle_1_deg	5.375
r_scangle_it	2.423
r_scbond_it	1.389
r_angle_refined_deg	1.152
r_mcangle_it	0.91
r_angle_other_deg	0.894
r_mcbond_it	0.469

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.406
r_dihedral_angle_4_deg	19.242
r_dihedral_angle_3_deg	15.597
r_dihedral_angle_1_deg	5.375
r_scangle_it	2.423
r_scbond_it	1.389
r_angle_refined_deg	1.152
r_mcangle_it	0.91
r_angle_other_deg	0.894
r_mcbond_it	0.469
r_mcbond_other	0.077
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14763
Nucleic Acid Atoms
Solvent Atoms	851
Heterogen Atoms	64

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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.