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the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P9L PDB ENTRY 1P9L (MONOMER)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 100 mM Tris/HCl, 26 % PEG 3350, 140 mM MgCl2 + 3 mM NADH in the protein solution, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 238.6 α = 90 b = 67.52 β = 117.08 c = 154.49 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 MARRESEARCH 2003-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8042 EMBL/DESY, HAMBURG X13
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 2.34 99 86.6 0.091 18.7 18.9 80382 80382 -3 -3 36.5
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 2.34 2.38 76.6 0.301 3.3 3491
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 (MONOMER) 2.34 30 77923 77923 2428 86.57 0.18307 0.18307 0.18134 0.1794 0.2381 0.234 RANDOM 41.528
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] 0.24 -1.04 -0.43 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 15.971 r_dihedral_angle_1_deg 5.597 r_scangle_it 5.141 r_scbond_it 3.313 r_angle_refined_deg 1.384 r_mcangle_it 1.202 r_mcbond_it 0.642 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 15.971 r_dihedral_angle_1_deg 5.597 r_scangle_it 5.141 r_scbond_it 3.313 r_angle_refined_deg 1.384 r_mcangle_it 1.202 r_mcbond_it 0.642 r_nbtor_refined 0.301 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.13 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14428 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 358
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing