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Structure of EstD11 in complex with Naproxen
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 3.2M Sodium formate + 0.1M citrate pH 5
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.172 α = 90 b = 90.604 β = 90 c = 126.251 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 2020-05-13 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 1.7 45.3 100 0.109 0.031 0.999 18.9 13.2 30890
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 1.7 1.73 100 0.95 0.277 0.91 3.1 12.6
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 7AT0 1.7 45.048 30878 1548 99.948 0.158 0.156 0.1701 0.1908 0.1981 19.281
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] -0.012 0.011 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.89 r_dihedral_angle_4_deg 23.204 r_dihedral_angle_3_deg 14.403 r_lrange_it 6.707 r_lrange_other 6.494 r_dihedral_angle_1_deg 5.901 r_scangle_it 4.86 r_scangle_other 4.858 r_scbond_other 3.248 r_scbond_it 3.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.89 r_dihedral_angle_4_deg 23.204 r_dihedral_angle_3_deg 14.403 r_lrange_it 6.707 r_lrange_other 6.494 r_dihedral_angle_1_deg 5.901 r_scangle_it 4.86 r_scangle_other 4.858 r_scbond_other 3.248 r_scbond_it 3.247 r_mcangle_other 2.402 r_mcangle_it 2.399 r_angle_refined_deg 1.712 r_mcbond_other 1.678 r_mcbond_it 1.677 r_angle_other_deg 1.46 r_symmetry_nbd_refined 0.265 r_nbd_other 0.244 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.217 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.168 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2243 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing