4C5J

Structure of the pyridoxal kinase from Staphylococcus aureus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I5B	PDB ENTRY 2I5B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				50 MM HEPES, PH 7.6, 2M AMMONIUM SULPHATE 10MG/ML PROTEIN

Crystal Properties
Matthews coefficient	Solvent content
2.28	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.58	α = 90
b = 102.34	β = 90.98
c = 83.54	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	PIXEL	DECTRIS PILATUS		2013-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	1.45	45.69	97.1	0.05	15.93	4.5		183201		1.5

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	1.45	1.5	93		0.86	1.87	4.4

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 2I5B	1.45	45.69	173936	9265	97.11	0.1325	0.13004	0.17811	RANDOM	21.437

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]
0.79		-0.46	-1.06		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.433
r_sphericity_free	26.463
r_dihedral_angle_4_deg	22.757
r_sphericity_bonded	13.697
r_dihedral_angle_3_deg	11.995
r_dihedral_angle_1_deg	6.119
r_rigid_bond_restr	5.817
r_scangle_other	5.703
r_long_range_B_refined	5.583
r_scbond_it	5.283
r_long_range_B_other	5.28
r_scbond_other	4.983
r_mcangle_other	4.317
r_mcangle_it	4.316
r_mcbond_it	3.535
r_mcbond_other	3.533
r_angle_refined_deg	1.802
r_angle_other_deg	0.905
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8290
Nucleic Acid Atoms
Solvent Atoms	992
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing