3F4N

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N5W	PDB code 1N5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	0.2 M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3,350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.627	α = 90
b = 114.818	β = 90
c = 154.316	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	CCD	SBC-3	mirrors	2008-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9793	APS	19-BM

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	2.402	34.81	95.6	0.108	7.3	6.7	75718	75718			42.08

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	2.402	2.44	88.7		0.6	2.1	5.5	3435

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 1N5W	2.402	34.81	71176	71176	3763	94.58	0.195	0.195	0.191	0.266	RANDOM	23.632

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]
-1.69			2.58		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.567
r_dihedral_angle_4_deg	18.946
r_dihedral_angle_3_deg	18.486
r_dihedral_angle_1_deg	6.475
r_scangle_it	4.188
r_scbond_it	2.586
r_angle_refined_deg	1.792
r_mcangle_it	1.467
r_mcbond_it	0.79
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14621
Nucleic Acid Atoms
Solvent Atoms	667
Heterogen Atoms	143

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling