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Haloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous (T148L+G171Q+A172V+C176G)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 290 sodium acetate trihydrate, ammonium acetate, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.585 α = 115.47 b = 44.477 β = 98.79 c = 46.508 γ = 109.12
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2013-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.541790
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 1.69 39.42 92.2 0.057 18.76 2.8 30835 28416 16.8
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 1.69 1.73 87.7 0.17 9.16 2.7
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 3G9X 1.69 39.42 26995 1421 92.61 0.12295 0.12015 0.1201 0.17573 0.1752 RANDOM 10.459
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] -0.01 -0.01 0.01 0.03 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_4_deg 20.548 r_dihedral_angle_3_deg 12.812 r_sphericity_bonded 10.696 r_dihedral_angle_1_deg 5.774 r_rigid_bond_restr 4.112 r_long_range_B_refined 3.449 r_scbond_it 2.244 r_angle_refined_deg 1.846 r_mcangle_it 1.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_4_deg 20.548 r_dihedral_angle_3_deg 12.812 r_sphericity_bonded 10.696 r_dihedral_angle_1_deg 5.774 r_rigid_bond_restr 4.112 r_long_range_B_refined 3.449 r_scbond_it 2.244 r_angle_refined_deg 1.846 r_mcangle_it 1.408 r_mcbond_it 1.103 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2365 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing