☰ Navigation Tabs
Crystal structure of human heparanase in complex with competitive inhibitor GD05
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PRT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.838 α = 90 b = 71.188 β = 98.375 c = 78.628 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 EIGER2 XE 16M 2020-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 Diamond I03
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 2.05 37.677 99.6 0.993 6.2 6.7 30692
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 2.05 2.11 0.672
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 7PRT 2.05 37.677 30674 1488 99.549 0.226 0.2235 0.2303 0.2674 0.2717 45.913
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] 2.055 4.443 -5.089 1.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.534 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_4_deg 14.252 r_dihedral_angle_1_deg 7.408 r_lrange_it 6.662 r_lrange_other 6.658 r_scangle_other 4.932 r_scangle_it 4.931 r_mcangle_it 4.42 r_mcangle_other 4.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.534 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_4_deg 14.252 r_dihedral_angle_1_deg 7.408 r_lrange_it 6.662 r_lrange_other 6.658 r_scangle_other 4.932 r_scangle_it 4.931 r_mcangle_it 4.42 r_mcangle_other 4.419 r_scbond_other 3.211 r_scbond_it 3.21 r_mcbond_it 3.092 r_mcbond_other 3.09 r_angle_refined_deg 1.501 r_angle_other_deg 1.261 r_chiral_restr_other 0.406 r_symmetry_xyhbond_nbd_refined 0.252 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.205 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.188 r_nbd_other 0.185 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.065 r_xyhbond_nbd_other 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3627 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing