3M3H | pdb_00003m3h

1.75 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor'

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	295	7.7 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Classic II condition (CS2) A8 (#8). Cryo condition 2.5 M KCl and 25% sucrose. VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.762	α = 90
b = 56.762	β = 90
c = 113.708	γ = 90

Symmetry
Space Group	P 41 21 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	2010-03-04	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	1.75	30	99.4	0.063	27.8	13.7	19414	19414		-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	1.75	1.78	100		0.524	5.7	13.4	960

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	3DEZ	1.75	28.43	18360	18360	990	99.42	0.18136	0.1792	0.1893	0.22285	0.2284	RANDOM	19.589

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]
-0.76			-0.76		1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.986
r_dihedral_angle_4_deg	10.885
r_dihedral_angle_3_deg	9.596
r_scangle_it	4.595
r_dihedral_angle_1_deg	3.341
r_scbond_it	2.766
r_mcangle_it	1.643
r_angle_refined_deg	1.28
r_mcbond_it	0.843
r_angle_other_deg	0.778
r_mcbond_other	0.231
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1546
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	7

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling