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Crystallographic structure of a bacterial heparanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.8 M potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.03 α = 90 b = 125.03 β = 90 c = 125.16 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 CCD ADSC QUANTUM 210r 2012-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 31.29 99.4 6.9 14.54 129599
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 3VNZ 1.6 31.29 122996 6514 99.37 0.16563 0.16426 0.177 0.19187 0.204 RANDOM 19.61
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.18 r_dihedral_angle_4_deg 17.915 r_dihedral_angle_3_deg 12.118 r_long_range_B_refined 5.996 r_long_range_B_other 5.996 r_dihedral_angle_1_deg 5.99 r_scangle_other 2.37 r_mcangle_it 2.02 r_mcangle_other 2.02 r_scbond_it 1.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.18 r_dihedral_angle_4_deg 17.915 r_dihedral_angle_3_deg 12.118 r_long_range_B_refined 5.996 r_long_range_B_other 5.996 r_dihedral_angle_1_deg 5.99 r_scangle_other 2.37 r_mcangle_it 2.02 r_mcangle_other 2.02 r_scbond_it 1.469 r_scbond_other 1.468 r_angle_refined_deg 1.321 r_mcbond_it 1.226 r_mcbond_other 1.221 r_angle_other_deg 0.783 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6319 Nucleic Acid Atoms Solvent Atoms 1223 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing