2CZF

Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3 complexed with XMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1M HEPES(pH7.0), 29% Jeffamine ED-2001 reagent(pH7.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.054	α = 90
b = 73.134	β = 100.84
c = 61.979	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	RIGAKU JUPITER 210	Two dimensional focusing mirror	2005-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.00	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.85	50	95.1	0.047	22.27	3.25		31433		-3	18.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	80		0.259	3.09	2.4	2654

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2CZ5	1.85	46.79	29838	2978	90.1	0.208	0.242	RANDOM	29.3

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]
-5.92		-0.56	9.38		-3.46

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_scangle_it	4.01
c_scbond_it	3.09
c_mcangle_it	2.83
c_mcbond_it	2.04
c_angle_deg	1.4
c_improper_angle_d	1
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3196
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	48

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

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 R01GM133198.