3MVN

Crystal structure of a domain from a putative UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase from Haemophilus ducreyi 35000HP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52942 M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.6123.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.996α = 90
b = 46.996β = 90
c = 106.628γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMIRROR2010-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97872APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.920.6299.20.080.0840.48913.71000710007-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.931000.4460.4467.114.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.920.629943946447999.210.16220.15880.23707RANDOM23.008
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.096
r_dihedral_angle_4_deg15.132
r_dihedral_angle_3_deg14.194
r_scangle_it5.915
r_dihedral_angle_1_deg5.707
r_scbond_it3.812
r_mcangle_it2.313
r_rigid_bond_restr1.766
r_mcbond_it1.45
r_angle_refined_deg1.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.096
r_dihedral_angle_4_deg15.132
r_dihedral_angle_3_deg14.194
r_scangle_it5.915
r_dihedral_angle_1_deg5.707
r_scbond_it3.812
r_mcangle_it2.313
r_rigid_bond_restr1.766
r_mcbond_it1.45
r_angle_refined_deg1.412
r_angle_other_deg0.956
r_mcbond_other0.442
r_chiral_restr0.088
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms950
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing