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Crystal Structure of the S105A mutant of a carbon-carbon bond hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with 3-Cl HOPDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 grid of sodium malonate (1.5-2.4 M), pH 6.5/7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.6 65.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.596 α = 90 b = 66.596 β = 90 c = 338.179 γ = 120
Symmetry Space Group P 65 2 2
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 300 mm CCD 2008-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 57.64 97.5 30472 30456 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 97.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.02 57.64 30472 28184 1515 97.48 0.21677 0.21454 0.232 0.25864 0.2703 RANDOM 40.414
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] 1.47 0.74 1.47 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.513 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 15.653 r_scangle_it 9.784 r_scbond_it 7.084 r_dihedral_angle_1_deg 7.024 r_mcangle_it 4.641 r_mcbond_it 3.144 r_angle_refined_deg 1.81 r_angle_other_deg 1.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.513 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 15.653 r_scangle_it 9.784 r_scbond_it 7.084 r_dihedral_angle_1_deg 7.024 r_mcangle_it 4.641 r_mcbond_it 3.144 r_angle_refined_deg 1.81 r_angle_other_deg 1.004 r_mcbond_other 0.956 r_chiral_restr 0.12 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2108 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing