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Crystal structure of a lactonase double 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 2.93 57.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.164 α = 90 b = 86.164 β = 90 c = 471.862 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 2015-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 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 2.38 25 99.1 0.059 0.064 0.023 11.3 6.9 42998
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 2.38 2.46 93.2 0.28 6.9
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 (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 3XZL 2.39 25 40427 2046 99.53 0.217 0.21434 0.2652 0.26977 0.3059 RANDOM 33.666
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] 0.83 0.42 0.83 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.472 r_dihedral_angle_3_deg 19.582 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_1_deg 8.936 r_long_range_B_refined 7.857 r_long_range_B_other 7.855 r_scangle_other 5.673 r_mcangle_it 4.274 r_mcangle_other 4.274 r_scbond_it 3.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.472 r_dihedral_angle_3_deg 19.582 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_1_deg 8.936 r_long_range_B_refined 7.857 r_long_range_B_other 7.855 r_scangle_other 5.673 r_mcangle_it 4.274 r_mcangle_other 4.274 r_scbond_it 3.913 r_scbond_other 3.913 r_mcbond_it 3.028 r_mcbond_other 3.027 r_angle_refined_deg 1.525 r_angle_other_deg 0.99 r_chiral_restr 0.118 r_gen_planes_refined 0.018 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5301 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction