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Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M MOPS, 0.1M HEPES; 0.3M MgCl2; 0.3M CaCl2; 20% PEG550MME; 10%PEG20K
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.937 α = 90 b = 125.937 β = 90 c = 213.818 γ = 120
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 2013-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972386 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 99.7 14.66 7.81 22938 22874
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 2.5 2.65 98.7 0.87 2.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WDQ 2.5 48.58 1144 99.72 0.1667 0.1651 0.1959 0.1744 RANDOM 59.36
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] 0.18 0.09 0.18 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.77 r_dihedral_angle_4_deg 19.475 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 5.827 r_mcangle_it 3.023 r_mcbond_it 2.018 r_mcbond_other 2.018 r_angle_refined_deg 1.602 r_angle_other_deg 1.058 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.77 r_dihedral_angle_4_deg 19.475 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 5.827 r_mcangle_it 3.023 r_mcbond_it 2.018 r_mcbond_other 2.018 r_angle_refined_deg 1.602 r_angle_other_deg 1.058 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4609 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing PDB_EXTRACT data extraction Coot model building SCALEPACK data scaling