3R89

Crystal structure of orotidine 5-phosphate decarboxylase from Anaerococcus prevotii DSM 20548

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	0.2M NaCl, 0.1 M Tris pH 7.0, 30% (w/v) PEG-3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.507	α = 90
b = 108.848	β = 90
c = 138.171	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	ADSC QUANTUM 315r		2010-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924	APS	19-ID

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	1.844	85.503	94.2	0.114	30.7	7.7	52163	49114		-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)
	1.844	1.88	92.9		0.774	2.72	6.2	2412

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.844	85.5	48644	48644	2488	93.37	0.1604	0.1604	0.1584	0.197	RANDOM	19.769

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]
0.33			0.47		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_dihedral_angle_4_deg	23.82
r_dihedral_angle_3_deg	13.706
r_dihedral_angle_1_deg	5.676
r_scangle_it	4.209
r_scbond_it	2.568
r_angle_refined_deg	1.388
r_mcangle_it	1.377
r_mcbond_it	0.761
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_dihedral_angle_4_deg	23.82
r_dihedral_angle_3_deg	13.706
r_dihedral_angle_1_deg	5.676
r_scangle_it	4.209
r_scbond_it	2.568
r_angle_refined_deg	1.388
r_mcangle_it	1.377
r_mcbond_it	0.761
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4604
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

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.