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Marine microorganism esterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 20% PEG 8000, 50mM Li2SO4, 50mM Na2SO4, MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67 α = 90 b = 67 β = 90 c = 62 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 PILATUS3 6M 2018-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97892 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.03 58.024 99.7 0.097 0.997 9.5 7.5 20051 60.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.08 95.8 2.13 0.354 4.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3bf8 2.03 58.02 20015 1052 99.597 0.203 0.1999 0.2007 0.2613 0.2622 68.586
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] -0.547 -0.273 -0.547 1.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_dihedral_angle_4_deg 22.927 r_dihedral_angle_3_deg 18.413 r_lrange_it 13.206 r_scangle_it 9.295 r_mcangle_it 7.387 r_scbond_it 6.542 r_dihedral_angle_1_deg 5.828 r_mcbond_it 5.358 r_angle_refined_deg 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_dihedral_angle_4_deg 22.927 r_dihedral_angle_3_deg 18.413 r_lrange_it 13.206 r_scangle_it 9.295 r_mcangle_it 7.387 r_scbond_it 6.542 r_dihedral_angle_1_deg 5.828 r_mcbond_it 5.358 r_angle_refined_deg 1.43 r_nbtor_refined 0.308 r_symmetry_xyhbond_nbd_refined 0.249 r_symmetry_nbd_refined 0.204 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.113 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2088 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing Coot model building DMMulti model building MOLREP phasing