3RU6 | pdb_00003ru6

1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF) from Campylobacter jejuni subsp. jejuni NCTC 11168

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		search model found using BALBES software

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 7.3 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization condition: The PACT suite (F3 (63): 0.2 M Sodium iodide, 0.1 M Bis Tris propane pH 6.5, 20 % w/v PEG3350). Mixed 1:1 v/v , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.598	α = 90
b = 108.308	β = 95.73
c = 97.707	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	Be Lenses/Diamond Laue Mono	2011-04-21	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	98.4	0.05	18.41	2.6	84340	84340		-3	26.2

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	97.5		0.564	1.86	2.5	4147

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	balbes	1.8	29.12	79775	79775	4208	98.41	0.17005	0.16837	0.18	0.20267	0.22	RANDOM	32.773

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]
-1.48		-0.69	0.55		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.559
r_dihedral_angle_4_deg	7.603
r_dihedral_angle_3_deg	7.077
r_scangle_it	3.499
r_scbond_it	2.087
r_dihedral_angle_1_deg	1.906
r_angle_refined_deg	1.503
r_mcangle_it	1.202
r_angle_other_deg	0.862
r_mcbond_it	0.631

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.559
r_dihedral_angle_4_deg	7.603
r_dihedral_angle_3_deg	7.077
r_scangle_it	3.499
r_scbond_it	2.087
r_dihedral_angle_1_deg	1.906
r_angle_refined_deg	1.503
r_mcangle_it	1.202
r_angle_other_deg	0.862
r_mcbond_it	0.631
r_mcbond_other	0.176
r_chiral_restr	0.104
r_bond_refined_d	0.011
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	6993
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	30

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	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.