☰ Navigation Tabs
Allosteric activation of human prekallikrein by apple domain disc rotation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 0.1M carboxylic acid, 0.1M Hepes/mops pH 7.5, 12.5%MPD, 12.5%PEG1000, 12.5%PEG3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.611 α = 90 b = 129.633 β = 90 c = 55.84 γ = 90
Symmetry Space Group P 21 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 PILATUS3 6M 2016-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 1.36 129.63 99.7 0.999 0.05 6.6 141376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 6.08 98 0.682 0.76 2.5 6.5
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 2F83 1.36 28.05 134463 7196 99.73 0.16887 0.16745 0.1768 0.19591 0.204 RANDOM 18.539
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] -0.13 0.01 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_4_deg 18.734 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 6.312 r_long_range_B_refined 5.924 r_long_range_B_other 5.567 r_scangle_other 4.076 r_scbond_it 2.844 r_scbond_other 2.836 r_mcangle_it 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_4_deg 18.734 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 6.312 r_long_range_B_refined 5.924 r_long_range_B_other 5.567 r_scangle_other 4.076 r_scbond_it 2.844 r_scbond_other 2.836 r_mcangle_it 2.75 r_mcangle_other 2.75 r_angle_refined_deg 2.038 r_mcbond_it 1.922 r_mcbond_other 1.922 r_angle_other_deg 1.551 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4653 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing