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crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P9L PDB ENTRY 1P9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 100 mM Tris/HCl, 24 % PEG 3350, 140 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.9 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.13 α = 90 b = 89.46 β = 90 c = 77.52 γ = 90
Symmetry Space Group P 21 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 MARRESEARCH 2003-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R
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 2.9 99 98.9 0.061 23.9 31.1 13831 13831 -3 -3 48.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 99.8 0.494 4 657
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1P9L 2.9 30 12552 12552 1237 98.9 0.20415 0.20415 0.19883 0.1878 0.25689 0.2405 RANDOM 59.521
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] 5.16 1.52 -6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.649 r_dihedral_angle_3_deg 18.89 r_dihedral_angle_4_deg 17.087 r_scangle_it 6.644 r_dihedral_angle_1_deg 6.622 r_scbond_it 3.915 r_angle_refined_deg 1.689 r_mcangle_it 1.367 r_mcbond_it 0.739 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.649 r_dihedral_angle_3_deg 18.89 r_dihedral_angle_4_deg 17.087 r_scangle_it 6.644 r_dihedral_angle_1_deg 6.622 r_scbond_it 3.915 r_angle_refined_deg 1.689 r_mcangle_it 1.367 r_mcbond_it 0.739 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.1 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3622 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing