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Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol
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 1.85 33.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.82 α = 90 b = 65.19 β = 90 c = 126.09 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 210 2006-05-11 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.5 63.043 98.4 0.097 5.2 4.3 40063 39855 10.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 92.9 0.193 0.193 3.6 2.8 5410
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1MJ5 1.5 36.35 39807 39807 2003 98.29 0.146 0.144 0.1548 0.176 0.1853 RANDOM 9.054
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 32.484 r_dihedral_angle_4_deg 20.709 r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 6.266 r_scangle_it 3.591 r_scbond_it 2.445 r_angle_refined_deg 1.843 r_mcangle_it 1.725 r_mcbond_it 1.336 r_angle_other_deg 1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.484 r_dihedral_angle_4_deg 20.709 r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 6.266 r_scangle_it 3.591 r_scbond_it 2.445 r_angle_refined_deg 1.843 r_mcangle_it 1.725 r_mcbond_it 1.336 r_angle_other_deg 1.086 r_symmetry_vdw_other 0.378 r_mcbond_other 0.376 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.228 r_nbd_other 0.216 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.136 r_symmetry_vdw_refined 0.133 r_nbtor_other 0.09 r_bond_refined_d 0.021 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 2312 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 6
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction