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Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule)
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 Reservoir solution (22% PEG 8000, 150 mM 2-Morpholinoethanesulfonic acid, pH 6.0, 70 mM calcium choride)
Protein solution (20 mM 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid, pH7.4, 120 mM sodium choride, 70 mM calcium choride)
Crystal Properties Matthews coefficient Solvent content 1.84 33.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.797 α = 90 b = 66.656 β = 105.177 c = 46.564 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 2023-12-16 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 1.03 44.94 97.4 0.049 0.054 0.021 0.999 17.4 6.6 103954 10.6
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 1.03 1.05 93.3 0.714 0.776 0.298 0.828 2.2 6.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.03 44.94 103922 5116 97.254 0.12 0.1193 0.1388 0.139 13.445
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] -0.395 -0.196 0.84 -0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.12 r_dihedral_angle_3_deg 12.215 r_lrange_it 9.045 r_lrange_other 8.235 r_dihedral_angle_2_deg 6.711 r_dihedral_angle_1_deg 6.657 r_scangle_it 5.52 r_scangle_other 5.519 r_mcangle_other 4.069 r_mcangle_it 4.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.12 r_dihedral_angle_3_deg 12.215 r_lrange_it 9.045 r_lrange_other 8.235 r_dihedral_angle_2_deg 6.711 r_dihedral_angle_1_deg 6.657 r_scangle_it 5.52 r_scangle_other 5.519 r_mcangle_other 4.069 r_mcangle_it 4.066 r_scbond_it 3.813 r_scbond_other 3.812 r_rigid_bond_restr 3.152 r_mcbond_it 2.794 r_mcbond_other 2.772 r_angle_refined_deg 1.691 r_angle_other_deg 0.65 r_nbd_other 0.206 r_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.19 r_symmetry_nbd_refined 0.165 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing