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Crystal structure of a possible dehydrogenase from Mycobacterium tuberculosis at 2.3A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9C pdb entry 1s9c modified with ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 290 Wizard screen condition g12, 1M Na/K tartrate, 100mM MES pH 6.0, MYTUD.00504.A AT 56MG/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.61 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.29 α = 90 b = 135.17 β = 90 c = 162.4 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944 2009-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 40 97.9 0.095 18.74 7.1 63818 62471 -3 35.15
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 2.36 80.4 0.514 3.7 4.4 4627
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1s9c modified with ccp4 program chainsaw 2.3 40 63818 62387 3166 97.9 0.209 0.209 0.206 0.263 0.2198 RANDOM 20.71
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] 0.45 1.52 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.767 r_dihedral_angle_4_deg 18.944 r_dihedral_angle_3_deg 13.197 r_dihedral_angle_1_deg 6.415 r_scangle_it 3.244 r_scbond_it 2.056 r_angle_refined_deg 1.565 r_mcangle_it 1.496 r_angle_other_deg 0.906 r_mcbond_it 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.767 r_dihedral_angle_4_deg 18.944 r_dihedral_angle_3_deg 13.197 r_dihedral_angle_1_deg 6.415 r_scangle_it 3.244 r_scbond_it 2.056 r_angle_refined_deg 1.565 r_mcangle_it 1.496 r_angle_other_deg 0.906 r_mcbond_it 0.819 r_mcbond_other 0.264 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8064 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 17
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling