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Crystal structure of LD transpeptidase LdtMt1 from M. tuberculosis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 1.24 M sodium phosphate and 0.16 M potassium phosphate, 10 mM TCEP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 57.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.246 α = 90 b = 67.246 β = 90 c = 119.748 γ = 90
Symmetry Space Group P 43 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 MARMOSAIC 225 mm CCD mirrors 2012-10-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.954, 0.9784, 0.9786, 0.9724 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 100 14669 14669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 100
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 MAD THROUGHOUT 2.2 15 13536 13536 974 99.99 0.16675 0.16356 0.175 0.21286 0.2222 RANDOM 23.128
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.938 r_dihedral_angle_4_deg 12.703 r_dihedral_angle_3_deg 11.335 r_dihedral_angle_1_deg 6.405 r_scangle_it 2.762 r_scbond_it 1.627 r_angle_refined_deg 1.185 r_mcangle_it 1.007 r_angle_other_deg 0.818 r_mcbond_it 0.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.938 r_dihedral_angle_4_deg 12.703 r_dihedral_angle_3_deg 11.335 r_dihedral_angle_1_deg 6.405 r_scangle_it 2.762 r_scbond_it 1.627 r_angle_refined_deg 1.185 r_mcangle_it 1.007 r_angle_other_deg 0.818 r_mcbond_it 0.519 r_mcbond_other 0.097 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1641 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling