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Crystal structure of a domain from a putative UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase from Haemophilus ducreyi 35000HP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 2 M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.61 23.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.996 α = 90 b = 46.996 β = 90 c = 106.628 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 MIRROR 2010-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 20.62 99.2 0.08 0.08 40.489 13.7 10007 10007 -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) Redundancy Number Unique Reflections (All) 1.9 1.93 100 0.446 0.446 7.1 14.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 20.62 9943 9464 479 99.21 0.1622 0.1588 0.23707 0.2494 RANDOM 23.008
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.096 r_dihedral_angle_4_deg 15.132 r_dihedral_angle_3_deg 14.194 r_scangle_it 5.915 r_dihedral_angle_1_deg 5.707 r_scbond_it 3.812 r_mcangle_it 2.313 r_rigid_bond_restr 1.766 r_mcbond_it 1.45 r_angle_refined_deg 1.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.096 r_dihedral_angle_4_deg 15.132 r_dihedral_angle_3_deg 14.194 r_scangle_it 5.915 r_dihedral_angle_1_deg 5.707 r_scbond_it 3.812 r_mcangle_it 2.313 r_rigid_bond_restr 1.766 r_mcbond_it 1.45 r_angle_refined_deg 1.412 r_angle_other_deg 0.956 r_mcbond_other 0.442 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 950 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing ARP/wARP model building Coot model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling DM phasing