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Crystal structure of human heparanase in complex with competitive inhibitor derrived from siastatin B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.11 α = 90 b = 70.92 β = 95.53 c = 78.56 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 PILATUS 6M-F 2015-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.917330 Diamond I04
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 1.7 45.938 99.6 0.998 10.8 1.9 55285
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 1.7 1.73 0.598
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 1.7 45.938 55284 2756 99.566 0.176 0.1743 0.2018 0.2077 0.2281 28.937
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] 1.357 0.28 -0.658 -0.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_4_deg 12.75 r_lrange_it 7.13 r_lrange_other 7.12 r_dihedral_angle_1_deg 6.809 r_scangle_it 5.372 r_scangle_other 5.371 r_mcangle_it 3.917 r_mcangle_other 3.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_4_deg 12.75 r_lrange_it 7.13 r_lrange_other 7.12 r_dihedral_angle_1_deg 6.809 r_scangle_it 5.372 r_scangle_other 5.371 r_mcangle_it 3.917 r_mcangle_other 3.916 r_scbond_it 3.514 r_scbond_other 3.514 r_mcbond_it 2.607 r_mcbond_other 2.607 r_angle_refined_deg 1.65 r_angle_other_deg 1.478 r_chiral_restr_other 0.494 r_symmetry_nbd_refined 0.354 r_symmetry_xyhbond_nbd_refined 0.259 r_nbd_refined 0.21 r_symmetry_nbd_other 0.192 r_nbd_other 0.192 r_xyhbond_nbd_other 0.171 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3640 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing