☰ Navigation Tabs
Coagulation factor Xa complex with a2-loop peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 imidazole, MPD
Crystal Properties Matthews coefficient Solvent content 1.96 37.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.473 α = 90 b = 72.419 β = 90 c = 82.335 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 XE 16M 2024-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.70979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.2 54.38 98.1 0.069 0.998 14.3 13.7 89301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 96.5 0.633 0.672 1.3 14.4
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 1.2 54.378 89240 4536 97.832 0.143 0.1413 0.1493 0.1718 0.173 17.469
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] -0.834 0.851 -0.017
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.306 r_lrange_other 15.304 r_dihedral_angle_6_deg 14.886 r_dihedral_angle_2_deg 12.079 r_dihedral_angle_3_deg 11.676 r_scangle_it 10.601 r_scangle_other 10.598 r_mcangle_it 8.127 r_mcangle_other 8.125 r_scbond_it 7.564
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.306 r_lrange_other 15.304 r_dihedral_angle_6_deg 14.886 r_dihedral_angle_2_deg 12.079 r_dihedral_angle_3_deg 11.676 r_scangle_it 10.601 r_scangle_other 10.598 r_mcangle_it 8.127 r_mcangle_other 8.125 r_scbond_it 7.564 r_scbond_other 7.561 r_dihedral_angle_1_deg 6.652 r_mcbond_it 5.816 r_mcbond_other 5.815 r_rigid_bond_restr 4.06 r_angle_refined_deg 1.977 r_angle_other_deg 0.731 r_dihedral_angle_other_2_deg 0.728 r_nbd_refined 0.319 r_xyhbond_nbd_refined 0.288 r_symmetry_nbd_refined 0.284 r_symmetry_nbd_other 0.228 r_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_other 0.149 r_metal_ion_refined 0.121 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing