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Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)
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, 20 % PEG 3350, 120 mM MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.26 α = 90 b = 122 β = 90 c = 77.93 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 2004-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.10 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 2.3 99 99.6 0.085 17.1 63.1 25757 25757 -3 -3 42.4
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 2.3 2.34 99.1 0.733 1.75 1256
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 2.3 30 24648 24648 1056 99.65 0.20697 0.20697 0.20514 0.1931 0.24924 0.236 RANDOM 54.607
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] 3.79 -3.04 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.483 r_dihedral_angle_4_deg 22.779 r_dihedral_angle_3_deg 16.758 r_scangle_it 6.212 r_dihedral_angle_1_deg 5.941 r_scbond_it 3.924 r_mcangle_it 1.547 r_angle_refined_deg 1.529 r_mcbond_it 0.854 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.483 r_dihedral_angle_4_deg 22.779 r_dihedral_angle_3_deg 16.758 r_scangle_it 6.212 r_dihedral_angle_1_deg 5.941 r_scbond_it 3.924 r_mcangle_it 1.547 r_angle_refined_deg 1.529 r_mcbond_it 0.854 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3648 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing