☰ Navigation Tabs
Crystal structure of Entamoeba histolytica serine protease inhibitor, Histopin, in the cleaved conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 25% Polyethylene glycol monomethyl ether 2000, 0.2M Potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 1.96 37.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.13 α = 90 b = 61.01 β = 90 c = 137.253 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 PIXEL DECTRIS EIGER X 4M 2018-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.83 45.64 98.5 0.066 0.998 17.2 7.3 29415
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 1.83 1.87 92 0.977 7.1
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 3NDA 1.83 45.64 27803 1508 98.15 0.1591 0.1568 0.165 0.203 0.2059 RANDOM 18.274
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] -0.24 -0.64 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_3_deg 14.194 r_dihedral_angle_1_deg 6.932 r_dihedral_angle_4_deg 6.375 r_angle_refined_deg 1.742 r_angle_other_deg 1.456 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_3_deg 14.194 r_dihedral_angle_1_deg 6.932 r_dihedral_angle_4_deg 6.375 r_angle_refined_deg 1.742 r_angle_other_deg 1.456 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2926 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing