3R38

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)
TypeSourceAccession CodeDetails
experimental modelPDB 2RL2PDB ENTRY 2RL2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52977.6 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 coefficientSolvent content
2.8156.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.579α = 90
b = 51.923β = 110.95
c = 78.178γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBe-Lenses/Diamond Laue Mono2011-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.233099.90.08314.333.72637026370-335.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.232.291000.363.693.71309

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2RL22.2329.112503525035132898.710.198410.196270.23864RANDOM38.984
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]
-3.86-0.730.083.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.709
r_dihedral_angle_4_deg5.724
r_dihedral_angle_3_deg5.307
r_scangle_it4.806
r_scbond_it2.921
r_mcangle_it1.597
r_angle_refined_deg1.328
r_dihedral_angle_1_deg0.96
r_mcbond_it0.818
r_angle_other_deg0.769
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.709
r_dihedral_angle_4_deg5.724
r_dihedral_angle_3_deg5.307
r_scangle_it4.806
r_scbond_it2.921
r_mcangle_it1.597
r_angle_refined_deg1.328
r_dihedral_angle_1_deg0.96
r_mcbond_it0.818
r_angle_other_deg0.769
r_mcbond_other0.199
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3283
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms51

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling