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Crystal structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant (L95V, A172V).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FBW PDB entry 3FBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 279 35 % (w/v) PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.663 α = 115.28 b = 44.489 β = 98.61 c = 46.389 γ = 109.55
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 2012-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.978 BESSY 14.2
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 50 91.7 0.035 18.85 2.6 78455 7.6
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 72.1 0.191 2.5 1.9
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3FBW 1.2 17.17 74518 3937 91.63 0.12185 0.12185 0.12007 0.1209 0.15495 0.1551 RANDOM 14.122
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] 0.19 0.09 0.17 0.23 0.19 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.803 r_dihedral_angle_4_deg 18.44 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_1_deg 5.773 r_sphericity_free 5.659 r_sphericity_bonded 4.208 r_scangle_it 3.365 r_scbond_it 2.57 r_mcangle_it 1.819 r_rigid_bond_restr 1.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.803 r_dihedral_angle_4_deg 18.44 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_1_deg 5.773 r_sphericity_free 5.659 r_sphericity_bonded 4.208 r_scangle_it 3.365 r_scbond_it 2.57 r_mcangle_it 1.819 r_rigid_bond_restr 1.777 r_angle_refined_deg 1.531 r_mcbond_it 1.296 r_nbtor_refined 0.323 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2350 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 10
Software Software Software Name Purpose MarDB data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling