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Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 The reservoir solution contains 0.1 M MES pH 6.0, 20% PEG8000, and 70 mM CaCl2. After clystals were grown, the reservoir solution containing 20 mM GPRP was added to the drop.
Crystal Properties Matthews coefficient Solvent content 1.86 33.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.897 α = 90 b = 66.947 β = 98.29 c = 91.428 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M Focusing Mirror 2024-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.32 45.24 97.7 0.081 0.088 0.033 0.999 14.9 6.9 100678 11.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.34 1.07 1.16 0.442 0.63 2 6.7
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 1.32 45.24 100641 5054 97.484 0.171 0.1694 0.1694 0.2033 0.2034 RANDOM 18.756
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] -0.934 -0.094 1.948 -0.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.467 r_dihedral_angle_3_deg 12.132 r_lrange_it 11.746 r_dihedral_angle_1_deg 6.719 r_scangle_it 5.88 r_mcangle_it 5.661 r_dihedral_angle_2_deg 5.488 r_scbond_it 3.793 r_mcbond_it 3.577 r_rigid_bond_restr 3.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.467 r_dihedral_angle_3_deg 12.132 r_lrange_it 11.746 r_dihedral_angle_1_deg 6.719 r_scangle_it 5.88 r_mcangle_it 5.661 r_dihedral_angle_2_deg 5.488 r_scbond_it 3.793 r_mcbond_it 3.577 r_rigid_bond_restr 3.011 r_angle_refined_deg 1.355 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.229 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.121 r_chiral_restr 0.083 r_metal_ion_refined 0.074 r_gen_planes_refined 0.007 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4034 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing