3PAJ | pdb_00003paj

2.00 Angstrom resolution crystal structure of a quinolinate phosphoribosyltransferase from Vibrio cholerae O1 biovar eltor str. N16961

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	287	Protein: 7 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: 0.2 M MgCl2, 0.1 M Bis-Tris, 25 % (w/v) PEG3350. Mixed 1:1 v/v., VAPOR DIFFUSION, SITTING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.195	α = 90
b = 79.551	β = 90
c = 117.908	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	MARMOSAIC 225 mm CCD	Be-Lenses/Diamond Laue Mono	2010-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	30	99.8	0.081	22.98	7.1	38142	38142		-3	21.6

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	2.03	100		0.279	9.76	7.3	1893

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 1QAP	2	29.6	36159	36159	1908	99.68	0.17557	0.17312	0.1851	0.22175	0.234	RANDOM	26.541

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]
0.69			-0.92		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.254
r_dihedral_angle_4_deg	10.904
r_dihedral_angle_3_deg	9.32
r_scangle_it	4.062
r_scbond_it	2.406
r_dihedral_angle_1_deg	2.058
r_angle_refined_deg	1.609
r_mcangle_it	1.323
r_angle_other_deg	0.973
r_mcbond_it	0.69
r_mcbond_other	0.185
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4542
Nucleic Acid Atoms
Solvent Atoms	414
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling