3HYO | pdb_00003hyo

Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H74	PDB entry 3H74

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.2M MgCl2, 0.1M HEPES pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.594	α = 90
b = 69.761	β = 90
c = 132.924	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 210	Mirrors	2009-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.979	NSLS	X12C

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	1.85	24.06	99.8	0.05	13.5	9	26063	24694			29.7

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)
	1.849	1.897	100		0.313	6.8	7.9	2540

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 (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 3H74	1.85	24.06	26063	24694	1324	100	0.18208	0.17989	0.1879	0.22219	0.2243	RANDOM	22.158

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]
			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.989
r_dihedral_angle_4_deg	18.587
r_dihedral_angle_3_deg	12.313
r_dihedral_angle_1_deg	5.531
r_scangle_it	3.754
r_scbond_it	2.525
r_mcangle_it	1.6
r_angle_refined_deg	1.478
r_mcbond_it	1.11
r_nbtor_refined	0.305
r_xyhbond_nbd_refined	0.208
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.186
r_symmetry_hbond_refined	0.131
r_metal_ion_refined	0.103
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2045
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	28

Software

Software
Software Name	Purpose
CBASS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling