☰ Navigation Tabs
Crystal structure of histidine-rich glycoprotein N2 domain reveals redox activity at an interdomain disulfide bridge: Implications for the regulation of angiogenesis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 22.5% PEG MME 5000, 0.073M POTASSIUM SODIUM TARTRATE, 0.1M MES PH6.5
Crystal Properties Matthews coefficient Solvent content 4.33 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.138 α = 90 b = 77.138 β = 90 c = 69.36 γ = 120
Symmetry Space Group P 31 2 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 2M TORPIDAL MIRROR 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.93 33.71 93.2 0.05 11.3 4.1 17163 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2 69.2 0.33 2.1 2.7
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 SAD THROUGHOUT NONE 1.93 33.71 16201 863 93.2 0.18671 0.18472 0.1936 0.22524 0.2304 RANDOM 42.806
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] 0.79 0.39 0.79 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.904 r_dihedral_angle_4_deg 17.99 r_dihedral_angle_3_deg 12.088 r_dihedral_angle_1_deg 6.784 r_scbond_it 3.693 r_mcangle_it 2.43 r_angle_other_deg 2.394 r_angle_refined_deg 2.019 r_mcbond_it 1.712 r_mcbond_other 1.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.904 r_dihedral_angle_4_deg 17.99 r_dihedral_angle_3_deg 12.088 r_dihedral_angle_1_deg 6.784 r_scbond_it 3.693 r_mcangle_it 2.43 r_angle_other_deg 2.394 r_angle_refined_deg 2.019 r_mcbond_it 1.712 r_mcbond_other 1.679 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_other 0.015 r_gen_planes_refined 0.009 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 941 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing