3JZE

1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein solution: 6.8 mg/mL, 0.25 Sodium chloride, Tris-HCl pH 8.3. Screen solution: PEGs II, condition B10, 0.1M Sodium acetate, 0.1M MES pH 6.5, 30% w/v PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.437	α = 90
b = 79.486	β = 90.35
c = 180.61	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 300 mm CCD	Beryllium lenses	2009-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.8	30	98.6	0.083	13	3.7	130226	130226		-3	24.5

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	1.8	1.83	97.4		0.397	2.6	3.1	6322

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 entry 2EG6	1.8	29.83	123600	123600	6556	98.48	0.16547	0.16547	0.16347	0.20301	RANDOM	16.325

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]
1.01		-0.58	1.74		-2.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.106
r_dihedral_angle_4_deg	10.515
r_dihedral_angle_3_deg	8.604
r_scangle_it	4.334
r_dihedral_angle_1_deg	2.871
r_scbond_it	2.828
r_mcangle_it	1.673
r_angle_refined_deg	1.516
r_mcbond_it	1.022
r_angle_other_deg	0.888

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.106
r_dihedral_angle_4_deg	10.515
r_dihedral_angle_3_deg	8.604
r_scangle_it	4.334
r_dihedral_angle_1_deg	2.871
r_scbond_it	2.828
r_mcangle_it	1.673
r_angle_refined_deg	1.516
r_mcbond_it	1.022
r_angle_other_deg	0.888
r_mcbond_other	0.346
r_chiral_restr	0.096
r_bond_refined_d	0.011
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	10728
Nucleic Acid Atoms
Solvent Atoms	1328
Heterogen Atoms	112

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.