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Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 Sodium formate 3.2M and citrate pH 5 0.1M
Crystal Properties Matthews coefficient Solvent content 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.999 α = 90 b = 89.705 β = 90 c = 125.762 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS PILATUS 6M 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
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 2.13 44.84 99.9 0.067 0.027 0.998 18.2 6.7 15581
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 100 0.231 0.09 0.989 8.2
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 7AT0 2.13 42.36 14812 768 99.74 0.17027 0.16738 0.1808 0.22773 0.2378 RANDOM 39.253
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] -2.33 4.43 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.465 r_dihedral_angle_4_deg 19.041 r_long_range_B_other 14.026 r_long_range_B_refined 13.991 r_dihedral_angle_3_deg 13.875 r_scangle_other 13.177 r_scbond_it 10.773 r_scbond_other 10.769 r_mcangle_other 7.515 r_mcangle_it 7.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.465 r_dihedral_angle_4_deg 19.041 r_long_range_B_other 14.026 r_long_range_B_refined 13.991 r_dihedral_angle_3_deg 13.875 r_scangle_other 13.177 r_scbond_it 10.773 r_scbond_other 10.769 r_mcangle_other 7.515 r_mcangle_it 7.492 r_mcbond_other 6.265 r_mcbond_it 6.263 r_dihedral_angle_1_deg 5.2 r_angle_refined_deg 1.237 r_angle_other_deg 1.049 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2247 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing