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Crystal Structure of the S105A mutant of a carbon-carbon bond hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with 5,8-diF 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 3.53 65.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.155 α = 90 b = 66.155 β = 90 c = 342.18 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 2.166 57.27 98.6 24889 24875 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.17 57.26 24540 1253 98.62 0.2066 0.2039 0.2073 0.2579 0.2542 RANDOM 48.4425
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] 1.23 0.62 1.23 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.467 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 14.219 r_scangle_it 7.661 r_dihedral_angle_1_deg 5.884 r_scbond_it 5.206 r_mcangle_it 3.305 r_mcbond_it 1.925 r_angle_refined_deg 1.488 r_angle_other_deg 0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.467 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 14.219 r_scangle_it 7.661 r_dihedral_angle_1_deg 5.884 r_scbond_it 5.206 r_mcangle_it 3.305 r_mcbond_it 1.925 r_angle_refined_deg 1.488 r_angle_other_deg 0.874 r_mcbond_other 0.495 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2108 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing