3UWQ | pdb_00003uwq

1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LDV	pdb entry 3LDV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	protein at 7 mg/mL in 10 mM Tris-HCl, 500 mM NaCl, 5 mM BME. Crystallization condition: the PACT Suite (A4: 0.1 M SPG buffer pH 7.0 25 % (w/v) PEG1500), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.14	α = 90
b = 96.944	β = 90
c = 104.082	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 300 mm CCD	Be-Lenses	2011-10-24	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	100	0.063	29.48	7.4	49918	49918		-3	23.6

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)
1	1.8	1.83	100		0.527	4.3	7.4	2440

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 3LDV	1.8	29.33	47123	47123	2516	99.98	0.15158	0.1502	0.16	0.17787	0.19	RANDOM	28.189

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]
0.88			-1.04		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.901
r_dihedral_angle_3_deg	6.576
r_dihedral_angle_4_deg	4.623
r_scangle_it	2.736
r_angle_refined_deg	1.631
r_scbond_it	1.598
r_dihedral_angle_1_deg	1.373
r_mcangle_it	0.94
r_angle_other_deg	0.917
r_mcbond_it	0.489

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.901
r_dihedral_angle_3_deg	6.576
r_dihedral_angle_4_deg	4.623
r_scangle_it	2.736
r_angle_refined_deg	1.631
r_scbond_it	1.598
r_dihedral_angle_1_deg	1.373
r_mcangle_it	0.94
r_angle_other_deg	0.917
r_mcbond_it	0.489
r_mcbond_other	0.121
r_chiral_restr	0.097
r_bond_refined_d	0.007
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	3389
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	129

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 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.