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Endothiapepsin complexed with Phe-reduced-Tyr peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GVX PDB ENTRY 1GVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 294 0.1 M sodium acetate, 63% saturated ammonium sulfate, 3 mg/ml enzyme, 2 mM inhibitor (dissolved initially in DMSO), pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.62 α = 90 b = 72.787 β = 108.54 c = 45.113 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 PSI PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.0435 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.35 28.32 98.2 0.047 0.047 14.8 3.3 69622 69622 11.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.38 84.1 0.571 0.571 2.1 2.3 4381
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1GVX 1.35 27.72 70843 66078 3576 98.42 0.1252 0.1231 0.1222 0.1649 0.1663 RANDOM 16.182
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] 0.06 -0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.192 r_dihedral_angle_2_deg 30.028 r_dihedral_angle_4_deg 23.079 r_sphericity_bonded 12.406 r_dihedral_angle_3_deg 11.02 r_dihedral_angle_1_deg 6.5 r_rigid_bond_restr 5.698 r_long_range_B_refined 5.363 r_long_range_B_other 5.351 r_scangle_other 4.011
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.192 r_dihedral_angle_2_deg 30.028 r_dihedral_angle_4_deg 23.079 r_sphericity_bonded 12.406 r_dihedral_angle_3_deg 11.02 r_dihedral_angle_1_deg 6.5 r_rigid_bond_restr 5.698 r_long_range_B_refined 5.363 r_long_range_B_other 5.351 r_scangle_other 4.011 r_scbond_it 3.814 r_scbond_other 3.808 r_mcangle_other 2.472 r_mcangle_it 2.466 r_angle_refined_deg 2.112 r_mcbond_it 2.059 r_mcbond_other 1.952 r_angle_other_deg 1.018 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2461 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 51
Software Software Software Name Purpose GDA data collection FFT model building REFMAC refinement XDS data reduction SCALA data scaling FFT phasing