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Structure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) from Rhodococcus rhodochrous
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BN6 PDB ENTRY 1BN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 25 % PEG 4 000, 8 % iso-propanol and 100 mM Na-Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.05 40.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.524 α = 115.48 b = 44.37 β = 98.41 c = 46.541 γ = 109.6
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 MIRROR: ELLIPTICALLY BENT 12 QUARTZ SEGMENTS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.2 20 90.7 0.05 29.6 3.4 77114 1 11.1
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 1.2 1.24 45 0.179 6.8 2.1
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 1BN6 1.22 20 77113 3872 94.4 0.132 0.13 0.1351 0.162 0.1449 RANDOM 8.817
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] 0.51 0.34 0.12 -0.08 0.1 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.902 r_dihedral_angle_4_deg 21.933 r_dihedral_angle_3_deg 14.245 r_sphericity_free 8.381 r_dihedral_angle_1_deg 5.863 r_sphericity_bonded 4.293 r_scangle_it 3.789 r_scbond_it 2.731 r_mcangle_it 2.058 r_mcbond_other 2.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.902 r_dihedral_angle_4_deg 21.933 r_dihedral_angle_3_deg 14.245 r_sphericity_free 8.381 r_dihedral_angle_1_deg 5.863 r_sphericity_bonded 4.293 r_scangle_it 3.789 r_scbond_it 2.731 r_mcangle_it 2.058 r_mcbond_other 2.025 r_angle_refined_deg 1.605 r_rigid_bond_restr 1.517 r_mcbond_it 1.433 r_angle_other_deg 0.974 r_symmetry_hbond_refined 0.242 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2393 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling