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Crystal structure of prethrombin-2 with a peptide corresponding to the C-terminus of the heavy chain of factor Va
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Prethrombin-2 and peptide sequences provided
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.2 M NaCl (Salt)
0.1 M TRIS 8.5 pH (Buffer)
25 %w/v PEG 3350 (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.03 39.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.416 α = 82.9 b = 51.567 β = 85.326 c = 65.992 γ = 65.901
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 2025-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7838 Diamond I03
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 2.8 38.76 99.2 0.244 0.95 3 3.7 15006
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 2.8 2.95 98.9 1.032 0.432 0.7 3.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 38.76 14980 719 99.074 0.261 0.2587 0.2644 0.3045 0.3064 RANDOM 47.074
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] -3.825 2.451 -0.426 -1.163 -2.27 6.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.18 r_dihedral_angle_6_deg 9.479 r_dihedral_angle_1_deg 6.001 r_dihedral_angle_2_deg 5.187 r_lrange_it 4.517 r_lrange_other 4.517 r_mcangle_it 2.387 r_mcangle_other 2.387 r_scangle_it 1.64 r_scangle_other 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.18 r_dihedral_angle_6_deg 9.479 r_dihedral_angle_1_deg 6.001 r_dihedral_angle_2_deg 5.187 r_lrange_it 4.517 r_lrange_other 4.517 r_mcangle_it 2.387 r_mcangle_other 2.387 r_scangle_it 1.64 r_scangle_other 1.64 r_mcbond_it 1.295 r_mcbond_other 1.295 r_scbond_it 0.85 r_scbond_other 0.85 r_angle_refined_deg 0.785 r_angle_other_deg 0.266 r_nbd_other 0.262 r_symmetry_nbd_refined 0.255 r_xyhbond_nbd_refined 0.251 r_symmetry_nbd_other 0.24 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.214 r_nbtor_refined 0.187 r_ncsr_local_group_2 0.138 r_ncsr_local_group_1 0.114 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.05 r_symmetry_xyhbond_nbd_other 0.007 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5114 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing