2AQ6 | pdb_00002aq6

X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 1.7 a resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	12% PEG 8000, 8% ethylene glycol, 30 mM KF, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.87	α = 90
b = 55.35	β = 107.77
c = 54.52	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	CCD	ADSC QUANTUM 4		2004-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1158	ALS	8.3.1

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	1.7	37.87	97.5	0.066		2.9	29370	28603			12.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	90.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.7	37.87	29370	28603	1390	97.5	0.191	0.191	0.1912	0.194	0.195	RANDOM	16.3

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]
-1.72		-0.83	-0.52		2.23

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.9
c_angle_deg	1.3
c_improper_angle_d	0.83
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2232
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	16

Software

Software
Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
SCALEPACK	data scaling
CNS	phasing