2DDM | pdb_00002ddm

Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene at 2.1 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TD2	PDB entry 1TD2, 1LHP, 1JXH
experimental model	PDB	1LHP	PDB entry 1TD2, 1LHP, 1JXH
experimental model	PDB	1JXH	PDB entry 1TD2, 1LHP, 1JXH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	21% PEG 4000, 100mM Tris-HCl, 200mM Na acetate, 40mM MgSO4, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.31	α = 90
b = 75.132	β = 90
c = 107.8	γ = 90

Symmetry
Space Group	P 21 21 21

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 II	mirrors	2004-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	2.1	61.6	99.3	0.067	9.8	4.5		31487			18.4

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)
	2.1	2.2	99.1		0.248	2.1	4.1	4009

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1TD2, 1LHP, 1JXH	2.1	19.75	31407	31407	1590	99.2	0.204	0.194	0.194	0.19	0.218	0.21	RANDOM	35.4

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]
-1.35			5.27		-3.91

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.8
c_angle_deg	1.2
c_improper_angle_d	0.77
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4112
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	16

Software

Software
Software Name	Purpose
CNS	refinement
bioteX	data reduction
bioteX	data scaling
CaspR	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.