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Crystal structure of Human HPSE1 in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 25% w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.38 α = 90 b = 71.049 β = 98.09 c = 78.28 γ = 90
Symmetry Space Group P 1 21 1
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 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00003 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 77.5 99.8 0.993 7.5 5.3 32623
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.79
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 THROUGHOUT 5E8M 2 43.977 32605 1600 99.807 0.168 0.1656 0.1787 0.2092 0.2209 32.783
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] -0.678 1.313 -3.109 3.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.751 r_dihedral_angle_4_deg 21.087 r_dihedral_angle_3_deg 14.579 r_lrange_it 8.651 r_lrange_other 8.651 r_dihedral_angle_1_deg 7.204 r_scangle_it 4.948 r_scangle_other 4.948 r_mcangle_other 3.939 r_mcangle_it 3.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.751 r_dihedral_angle_4_deg 21.087 r_dihedral_angle_3_deg 14.579 r_lrange_it 8.651 r_lrange_other 8.651 r_dihedral_angle_1_deg 7.204 r_scangle_it 4.948 r_scangle_other 4.948 r_mcangle_other 3.939 r_mcangle_it 3.935 r_scbond_it 3.2 r_scbond_other 3.199 r_mcbond_it 2.593 r_mcbond_other 2.57 r_angle_refined_deg 1.582 r_angle_other_deg 1.273 r_symmetry_xyhbond_nbd_refined 0.234 r_nbd_other 0.217 r_nbd_refined 0.201 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.168 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3644 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing