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Structure of haloalkane dehalogenase variant DhaA101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E46 PDB ENTRY 4E46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES/IMIDAZOLE PH 6.5, 10% (W/V) PEG 20000, 20% (V/V) PEG MME 500, 0.2 M DL-GLUTAMATIC ACID MONOHYDRATE, 0.02M DL-ALANINE, 0.02M GLYCINE, 0.02M DL-LYSINE MONOHYDROCHLORIDE AND 0.02M DL-SERINE
Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.66 α = 115.26 b = 44.4 β = 97.59 c = 46.26 γ = 109.52
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 2015-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 0.99 39.61 70.2 0.03 18.2 3.2 107099 2
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 0.99 1.02 6.5 0.33 2.1 1.3
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 4E46 0.99 39.61 101816 5283 70.18 0.11483 0.11405 0.1239 0.12973 0.1389 RANDOM 13.438
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] 0.06 0.32 0.41 -0.15 0.21 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.555 r_sphericity_free 28.241 r_dihedral_angle_4_deg 21.15 r_dihedral_angle_3_deg 13.011 r_sphericity_bonded 9.257 r_dihedral_angle_1_deg 6.003 r_rigid_bond_restr 3.756 r_scangle_it 2.348 r_angle_refined_deg 2.177 r_scbond_it 1.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.555 r_sphericity_free 28.241 r_dihedral_angle_4_deg 21.15 r_dihedral_angle_3_deg 13.011 r_sphericity_bonded 9.257 r_dihedral_angle_1_deg 6.003 r_rigid_bond_restr 3.756 r_scangle_it 2.348 r_angle_refined_deg 2.177 r_scbond_it 1.886 r_mcangle_it 1.674 r_mcbond_it 1.281 r_angle_other_deg 1.212 r_mcbond_other 1.069 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2357 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing