2AJP | pdb_00002ajp

Crystal structure of a human pyridoxal kinase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9.5	291	30% PEG550MME, pH 9.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.132	α = 90
b = 114.971	β = 90
c = 169.261	γ = 90

Symmetry
Space Group	I 2 2 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	CCD	ADSC QUANTUM 210		2005-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97972	APS	17-ID

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	2.3	50	97.8	0.121		6.7		38925

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	2.3	2.38		86.7	0.67		4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1RFV	2.5	46.078	31250	936	100	0.243	0.2414	0.2441	0.2834	0.287	thin shells	35.93

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]
2.592			-1.497		-1.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.244
r_dihedral_angle_4_deg	17.943
r_dihedral_angle_3_deg	16.644
r_dihedral_angle_1_deg	6.058
r_scangle_it	3.607
r_mcangle_it	3.562
r_scbond_it	2.604
r_mcbond_it	2.298
r_angle_refined_deg	1.411
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.256
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.004
r_metal_ion_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4589
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	104

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction