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Human heparanase in complex with neutralizing antibody A54 Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E8M heparanase experimental model PDB 1AE6 fab fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium Nitrate
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.738 α = 90 b = 69.738 β = 90 c = 429.781 γ = 90
Symmetry Space Group P 41 21 2
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 9M 2019-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.49 107.44 86.8 0.28 0.999 9.2 15 9227
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.49 3.87 2.25 0.95 1.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.49 107.44 9227 465 63.446 0.224 0.2197 0.2185 0.323 0.3212 143.262
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] -0.237 -0.237 0.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.776 r_dihedral_angle_6_deg 15.647 r_lrange_it 11.558 r_lrange_other 11.557 r_dihedral_angle_1_deg 6.65 r_scangle_it 5.684 r_scangle_other 5.684 r_mcangle_it 4.764 r_mcangle_other 4.763 r_scbond_it 3.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.776 r_dihedral_angle_6_deg 15.647 r_lrange_it 11.558 r_lrange_other 11.557 r_dihedral_angle_1_deg 6.65 r_scangle_it 5.684 r_scangle_other 5.684 r_mcangle_it 4.764 r_mcangle_other 4.763 r_scbond_it 3.238 r_scbond_other 3.238 r_dihedral_angle_2_deg 3.139 r_mcbond_it 2.76 r_mcbond_other 2.76 r_angle_refined_deg 1.813 r_angle_other_deg 0.628 r_nbd_other 0.27 r_symmetry_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.21 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_ext_dist_refined_b 0.079 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6983 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement xia2 data reduction STARANISO data scaling MOLREP phasing