3SG1 | pdb_00003sg1

2.6 Angstrom Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 (MurA1) from Bacillus anthracis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EJD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein solution: 7.7 mg/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3), Screen solution: PEG's II, condition D10, 0.2M Sodium acetate, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.666	α = 90
b = 125.217	β = 105.73
c = 79.472	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	MARMOSAIC 300 mm CCD	Beryllium lenses	2009-07-07	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	2.6	30	100	0.103	12.6	3.8	45804	45804		-3	45.4

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	2.6	2.64	100		0.509	2.7	3.8	2277

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	1EJD	2.6	29.88	43242	43242	2299	99.96	0.1836	0.1836	0.1798	0.19	0.25472	0.25	RANDOM	32.778

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]
0.7		0.45	-0.02		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.47
r_dihedral_angle_4_deg	9.342
r_dihedral_angle_3_deg	8.892
r_scangle_it	5.506
r_scbond_it	3.296
r_mcangle_it	1.937
r_dihedral_angle_1_deg	1.612
r_angle_refined_deg	1.27
r_mcbond_it	1.02
r_angle_other_deg	0.772

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.47
r_dihedral_angle_4_deg	9.342
r_dihedral_angle_3_deg	8.892
r_scangle_it	5.506
r_scbond_it	3.296
r_mcangle_it	1.937
r_dihedral_angle_1_deg	1.612
r_angle_refined_deg	1.27
r_mcbond_it	1.02
r_angle_other_deg	0.772
r_mcbond_other	0.312
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12624
Nucleic Acid Atoms
Solvent Atoms	494
Heterogen Atoms	23

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.