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Crystal structure of a lactonase mutant in complex with substrate a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 24% PEG 2000 MME, 0.1M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.94 58.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.205 α = 90 b = 86.205 β = 90 c = 473.247 γ = 120
Symmetry Space Group P 61 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 ADSC QUANTUM 315r 2015-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.97622 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.8 25 97.5 0.053 0.059 0.024 13.9 6.2 26370
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 2.8 2.9 98.9 0.163 6.3
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 3WZL 2.8 25 25085 1264 97.59 0.2063 0.20334 0.2299 0.26483 0.2825 RANDOM 36.008
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] 1.21 0.6 1.21 -3.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.983 r_dihedral_angle_3_deg 21.653 r_dihedral_angle_4_deg 18.292 r_dihedral_angle_1_deg 10.256 r_long_range_B_other 8.697 r_long_range_B_refined 8.694 r_mcangle_it 6.016 r_mcangle_other 6.015 r_scangle_other 5.494 r_mcbond_it 3.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.983 r_dihedral_angle_3_deg 21.653 r_dihedral_angle_4_deg 18.292 r_dihedral_angle_1_deg 10.256 r_long_range_B_other 8.697 r_long_range_B_refined 8.694 r_mcangle_it 6.016 r_mcangle_other 6.015 r_scangle_other 5.494 r_mcbond_it 3.832 r_mcbond_other 3.832 r_scbond_it 3.499 r_scbond_other 3.497 r_angle_refined_deg 1.5 r_angle_other_deg 0.969 r_chiral_restr 0.099 r_gen_planes_refined 0.017 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5199 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction