Experiment: 3TR2

Structure of a orotidine 5'-phosphate decarboxylase (pyrF) from Coxiella burnetii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ModelArchive	MA-CXT5E	ENTRY 1LDV that was moved from PDB to ModelArchive

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SITTING DROP	8.5	277	0.09 M Tris, pH 8.5, 0.17 M sodium acetate, 25.5% PEG4000, 15% glycerol, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.62	α = 90
b = 99.676	β = 90
c = 110.565	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	RIGAKU SATURN 944		2011-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2	30	98.2	0.056	10.9	4.1	31144	30584		-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	2	2.03	94.5		0.426		2.9	1474

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 (All)	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 1LDV	2.001	17.896	32670	30492	1535	98.03	0.1845	0.1845	0.1828	0.1758	0.217	0.2082	RANDOM	35.5438

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]
3.6271			-1.3553		-2.2718

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.146
f_angle_d	0.995
f_chiral_restr	0.065
f_bond_d	0.006
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3354
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling