4RV4 | pdb_00004rv4

2.65 Angstrom Resolution Crystal Structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor' in complex with 5-phospho-alpha-D-ribosyl diphosphate (PRPP)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M3H	PDB ID 3M3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	295	7 MG/ML PROTEIN IN 10 MM TRIS/HCL PH 8.0, 500 MM NACL, 5 MM BME, 10 MM 5-PHOSPHO-ALPHA-D-RIBOSYL DIPHOSPHATE (PRPP). CRYSTALS GREW FROM 0.1 M MIB BUFFER PH 4.0, 25% (W/V) PEG1500 (THE PACT SUITE CONDITION #13), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.268	α = 90
b = 133.268	β = 90
c = 151.348	γ = 90

Symmetry
Space Group	I 4 2 2

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	2010-08-19	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	2.65	30	90	0.066	20.82	6.6	18197	18197		-3	64.9

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	2.65	2.7	97.7		0.49	4.3	6.6	983

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-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 ID 3M3H	2.65	29.54	17278	919	89.85	0.19814	0.19581	0.19	0.24181	0.25	RANDOM	75.808

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]
-5.39			-5.39		10.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.542
r_dihedral_angle_4_deg	15.348
r_dihedral_angle_3_deg	9.296
r_dihedral_angle_1_deg	1.923
r_angle_refined_deg	1.645
r_angle_other_deg	1.128
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.542
r_dihedral_angle_4_deg	15.348
r_dihedral_angle_3_deg	9.296
r_dihedral_angle_1_deg	1.923
r_angle_refined_deg	1.645
r_angle_other_deg	1.128
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4693
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	73

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.