3N2L | pdb_00003n2l

2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LH0	PDB entry 1LH0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	295	7.5 mg/mL protein in 10 mM Tris/HCl pH 8.3 0.5 M NaCl, 5 mM BME. The crystallization condition is The Classics II Suite (#8) Cryo 5M NaCl + 50% sucrose. Crystals grew from 1:1 v/v drop. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.587	α = 90
b = 76.712	β = 92.63
c = 133.944	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	CCD	MARMOSAIC 225 mm CCD	Be Lenses/Diamond Laue Mono	2010-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97857	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	2.1	30	99.7	0.079	11.25	3.9	114128	114128		-3

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)
	2.1	2.14	99.6		0.495	2.72	3.7	5630

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 1LH0	2.1	30	108289	108289	5711	99.51	0.22436	0.222	0.26	0.26861	0.3	RANDOM	44.833

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]
-0.94		0.7	-2.37		3.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.681
r_dihedral_angle_4_deg	14.486
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	3.748
r_scangle_it	3.576
r_scbond_it	2.265
r_angle_refined_deg	1.567
r_mcangle_it	1.504
r_angle_other_deg	0.867
r_mcbond_it	0.837

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.681
r_dihedral_angle_4_deg	14.486
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	3.748
r_scangle_it	3.576
r_scbond_it	2.265
r_angle_refined_deg	1.567
r_mcangle_it	1.504
r_angle_other_deg	0.867
r_mcbond_it	0.837
r_mcbond_other	0.209
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11639
Nucleic Acid Atoms
Solvent Atoms	639
Heterogen Atoms	3

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.