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Structure of haloalkane dehalogenase variant DhaA80 from Rhodococcus rhodochrous
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1M BisTris propane, 0.2M Sodium Fluoride,20% PEG3350, 50% w/v 1-Butyl-3-methylimidazolium methyl sulfate
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.889 α = 90 b = 69.551 β = 90 c = 83.916 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 MARMOSAIC 225 mm CCD 2015-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.75 32.15 99.17 0.989 1.86 2 29090
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.792 0.369
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 4F60 1.75 32.15 29090 1532 99.17 0.20908 0.20827 0.218 0.2244 0.2324 RANDOM 29.616
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] -3.37 2.36 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.294 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 5.087 r_long_range_B_refined 4.977 r_long_range_B_other 4.945 r_scangle_other 1.303 r_mcangle_it 1.168 r_mcangle_other 1.168 r_angle_refined_deg 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.294 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 5.087 r_long_range_B_refined 4.977 r_long_range_B_other 4.945 r_scangle_other 1.303 r_mcangle_it 1.168 r_mcangle_other 1.168 r_angle_refined_deg 1.071 r_angle_other_deg 0.974 r_scbond_it 0.937 r_scbond_other 0.813 r_mcbond_it 0.698 r_mcbond_other 0.693 r_chiral_restr 0.067 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2343 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing