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The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XXX Wild-type M. tuberculosis DHDPS, PDB ENTRY 1XXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 2.0M ammonium sulfate, 100mM sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.83 α = 90 b = 188.83 β = 90 c = 130.43 γ = 90
Symmetry Space Group P 41 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 2008-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.000 MAX II I911-3
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 99 99.2 0.118 14.1 4.8 157209 155951
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) 2 2.052 97.6 0.589 2.5 4.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Wild-type M. tuberculosis DHDPS, PDB ENTRY 1XXX 2.1 28.51 151456 130491 4197 98.54 0.17926 0.17849 0.20389 0.2062 RANDOM 23.177
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] -0.55 -0.55 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.004 r_dihedral_angle_4_deg 17.352 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_1_deg 6.152 r_scangle_it 4.108 r_scbond_it 3.108 r_mcangle_it 1.607 r_angle_refined_deg 1.52 r_mcbond_it 1.043 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.004 r_dihedral_angle_4_deg 17.352 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_1_deg 6.152 r_scangle_it 4.108 r_scbond_it 3.108 r_mcangle_it 1.607 r_angle_refined_deg 1.52 r_mcbond_it 1.043 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12875 Nucleic Acid Atoms Solvent Atoms 1596 Heterogen Atoms 293
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling