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X-ray crystal structure of an L,D-transpeptidase from Mycobacterium tuberculosis H37Rv
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MCSG1 E9: 0.2 M calcium chloride, 20% PEG3350, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.85 33.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.24 α = 90 b = 46.44 β = 90 c = 111.17 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2013-01-26 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU SATURN 944+ 2013-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 1.65 50 99.1 0.052 18.23 4.2 28399 28136
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.65 46.48 28399 26663 1416 99.08 0.19753 0.19571 0.2061 0.23077 0.2407 RANDOM 21.014
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] -0.95 -0.35 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.807 r_dihedral_angle_4_deg 16.744 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_1_deg 6.3 r_angle_refined_deg 1.712 r_mcangle_it 1.547 r_scbond_it 1.094 r_angle_other_deg 0.929 r_mcbond_it 0.922 r_mcbond_other 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.807 r_dihedral_angle_4_deg 16.744 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_1_deg 6.3 r_angle_refined_deg 1.712 r_mcangle_it 1.547 r_scbond_it 1.094 r_angle_other_deg 0.929 r_mcbond_it 0.922 r_mcbond_other 0.922 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1644 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX model building REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing