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Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain A and B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 25% (w/v) PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-TRIS propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.433 α = 90 b = 27.638 β = 114.14 c = 67.99 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 ADSC QUANTUM 210 2012-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 1.46 33.7 98.9 0.038 34254 34254 2.8 2.8
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 1.456 1.493 98.9 0.489 0.489 2.8 2 34254
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1.46 33.7 2.8 2.8 32519 32519 1728 98.85 0.16525 0.16239 0.1667 0.21813 0.2192 RANDOM 16.55
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] 0.02 -0.22 0.28 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_sphericity_free 31.242 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 11.252 r_sphericity_bonded 10.183 r_dihedral_angle_1_deg 5.659 r_rigid_bond_restr 3.062 r_angle_refined_deg 1.44 r_angle_other_deg 0.928 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_sphericity_free 31.242 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 11.252 r_sphericity_bonded 10.183 r_dihedral_angle_1_deg 5.659 r_rigid_bond_restr 3.062 r_angle_refined_deg 1.44 r_angle_other_deg 0.928 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1455 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 10
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling