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Crystal Structure of GDSL Esterase of Photobacterium sp. J15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.10 M ammonium sulphate, 0.15 M sodium cacodylate trihydrate pH 6.5, and 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.42 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.182 α = 90 b = 66.461 β = 90 c = 105.468 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU 2016-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.38 56.23 98.2 0.07 0.07 0.912 25 2 70491
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 1.38 1.43 95.3 0.193 5.7 1.98
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 SAD THROUGHOUT 1.38 56.23 67010 3478 98.15 0.159 0.1579 0.1664 0.179 0.1871 RANDOM 12.254
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] -0.02 -0.36 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.138 r_dihedral_angle_4_deg 13.929 r_dihedral_angle_3_deg 13.269 r_dihedral_angle_1_deg 6.205 r_angle_refined_deg 2.524 r_angle_other_deg 1.183 r_chiral_restr 0.154 r_bond_refined_d 0.029 r_gen_planes_refined 0.012 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.138 r_dihedral_angle_4_deg 13.929 r_dihedral_angle_3_deg 13.269 r_dihedral_angle_1_deg 6.205 r_angle_refined_deg 2.524 r_angle_other_deg 1.183 r_chiral_restr 0.154 r_bond_refined_d 0.029 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 33
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing