6CTY | pdb_00006cty

Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EG6	PDB entry 2EG6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.2 uL 10 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG 2 condition #67 (0.15 M DL-malic acid, pH 7.0, 20% w/v PEG3350), equilibrated against 1.3 M sodium chloride solution in 96-well 3-drop crystallization plate (Swissci)

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.838	α = 90
b = 112.202	β = 90
c = 208.264	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	PIXEL	DECTRIS PILATUS3 X 6M		2016-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97923, 1.28241, 1.28908	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.4	50.01	93.8	0.088	0.088	0.096	0.037	7.5	6.1		81980		-3	41.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	94.1		0.622	0.622	0.68	0.265	0.778	2.1	6

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 (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 2EG6	2.41	50.01	73934	3921	88.81	0.1613	0.1594	0.17	0.1979	0.2	RANDOM	44.305

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]
0.11			-0.14		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	46.284
r_dihedral_angle_2_deg	35.118
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	11.789
r_dihedral_angle_1_deg	5.432
r_angle_refined_deg	1.209
r_angle_other_deg	0.859
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	46.284
r_dihedral_angle_2_deg	35.118
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	11.789
r_dihedral_angle_1_deg	5.432
r_angle_refined_deg	1.209
r_angle_other_deg	0.859
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16072
Nucleic Acid Atoms
Solvent Atoms	1064
Heterogen Atoms	57

Software

Software
Software Name	Purpose
LAUEGEN	data processing
SCALEPACK	data scaling
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

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.