☰ Navigation Tabs
Crystal structure of the zymogen of cathepsin D from Schistosoma mansoni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291.15 0.2M ammonium sulphate
0.1M BisTris, pH 6.0
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.727 α = 90 b = 112.807 β = 90 c = 114.235 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 CCD MARMOSAIC 225 mm CCD 2016-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 43.11 99.3 0.213 0.235 0.998 7.04 5.474 48059 29.409
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.26 97.4 0.742 0.511 1.97 5.52
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.13 43.11 48039 2100 99.505 0.202 0.1996 0.1996 0.2559 0.256 RANDOM 27.999
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] 0.019 -0.129 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.021 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 8.24 r_lrange_it 7.819 r_dihedral_angle_2_deg 7.547 r_scangle_it 6.016 r_mcangle_it 4.686 r_scbond_it 4.247 r_mcbond_it 3.199 r_angle_refined_deg 2.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.021 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 8.24 r_lrange_it 7.819 r_dihedral_angle_2_deg 7.547 r_scangle_it 6.016 r_mcangle_it 4.686 r_scbond_it 4.247 r_mcbond_it 3.199 r_angle_refined_deg 2.093 r_nbtor_refined 0.296 r_symmetry_nbd_refined 0.212 r_nbd_refined 0.183 r_chiral_restr 0.152 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.113 r_ncsr_local_group_1 0.11 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5639 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing