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Haloalkane dehalogenase DmxA from Marinobacter sp. ELB17 possessing a unique catalytic residue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.2M ammonium acetate, 30%(w/v) PEG 4000 and 0.1M sodium citrate tribasic dihydrate, additionally added sarcosine
Crystal Properties Matthews coefficient Solvent content 1.89 34.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.371 α = 90 b = 78.343 β = 90 c = 150.514 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 PIXEL DECTRIS PILATUS 6M-F silicon pixel array detector 2013-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9724 ESRF ID29
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 1.45 100 99.7 0.112 8.02 5.28 86980 21.048
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 1.45 1.49 99.9 0.621 5.52
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 4E46 1.45 75.26 86980 4589 99.71 0.1752 0.1732 0.1738 0.2138 0.2116 RANDOM 18.624
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 31.769 r_dihedral_angle_4_deg 19.918 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_1_deg 5.845 r_angle_refined_deg 1.927 r_angle_other_deg 1.098 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.769 r_dihedral_angle_4_deg 19.918 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_1_deg 5.845 r_angle_refined_deg 1.927 r_angle_other_deg 1.098 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling