3R38 | pdb_00003r38

2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RL2	PDB ENTRY 2RL2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	7.6 mg/mL protein in 10 mM Tris-HCl, 0.25 M sodium chloride, 5 mM BME. Crystallization condition: The Classics II Suite condition A5 (0.1 M HEPES, pH 7.5, 2 M ammonium sulfate). Cryo condition: 1:1 v/v 3.6 M ammonium sulfate : 50 % sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.579	α = 90
b = 51.923	β = 110.95
c = 78.178	γ = 90

Symmetry
Space Group	C 1 2 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 225 mm CCD	Be-Lenses/Diamond Laue Mono	2011-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

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	2.23	30	99.9	0.083	14.33	3.7	26370	26370		-3	35.6

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)
	2.23	2.29	100		0.36	3.69	3.7	1309

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	PDB ENTRY 2RL2	2.23	29.11	25035	25035	1328	98.71	0.19841	0.19627	0.2	0.23864	0.25	RANDOM	38.984

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]
-3.86		-0.73	0.08		3.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.709
r_dihedral_angle_4_deg	5.724
r_dihedral_angle_3_deg	5.307
r_scangle_it	4.806
r_scbond_it	2.921
r_mcangle_it	1.597
r_angle_refined_deg	1.328
r_dihedral_angle_1_deg	0.96
r_mcbond_it	0.818
r_angle_other_deg	0.769

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.709
r_dihedral_angle_4_deg	5.724
r_dihedral_angle_3_deg	5.307
r_scangle_it	4.806
r_scbond_it	2.921
r_mcangle_it	1.597
r_angle_refined_deg	1.328
r_dihedral_angle_1_deg	0.96
r_mcbond_it	0.818
r_angle_other_deg	0.769
r_mcbond_other	0.199
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3283
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	51

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.