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Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,2-dichloroethane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MJ5 pdb entry 1MJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 30% PEG 4000, 0.2M magnesium acetate, 0.1M Tris, 5% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.12 α = 90 b = 64.46 β = 90 c = 134.21 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2006-05-07 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
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 1.6 50 99.6 0.086 8 5 35880
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 1.6 1.66 99.9 0.554 3.28 4.9 3548
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1MJ5 1.6 30.26 35833 1794 99.58 0.145 0.143 0.1577 0.173 0.1825 RANDOM 12.701
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.236 r_dihedral_angle_4_deg 16.289 r_dihedral_angle_3_deg 11.703 r_dihedral_angle_1_deg 6.369 r_scangle_it 4.023 r_scbond_it 2.756 r_angle_refined_deg 1.942 r_mcangle_it 1.81 r_mcbond_it 1.412 r_angle_other_deg 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.236 r_dihedral_angle_4_deg 16.289 r_dihedral_angle_3_deg 11.703 r_dihedral_angle_1_deg 6.369 r_scangle_it 4.023 r_scbond_it 2.756 r_angle_refined_deg 1.942 r_mcangle_it 1.81 r_mcbond_it 1.412 r_angle_other_deg 1.093 r_mcbond_other 0.4 r_symmetry_vdw_other 0.359 r_symmetry_vdw_refined 0.303 r_nbd_refined 0.226 r_nbd_other 0.215 r_symmetry_hbond_refined 0.213 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.123 r_nbtor_other 0.091 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2327 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction