☰ Navigation Tabs
Fibrinogen domain dimer from human Fibrinogen-like protein 1 (FGL-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 10% PEG8000, 8% ETHYLENE GLYCOL,
0.1 M HEPES, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.012 α = 90 b = 39.777 β = 90 c = 65.766 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 X 6M SI 111 CRYSTAL 2021-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.74 37.14 97.7 0.094 9.6 5.6 24297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.78 78.7 0.63 2.1 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FZD 1.74 37.14 23578 684 97.57 0.16691 0.16553 0.21498 0.2254 RANDOM 30.048
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] 0.09 0.06 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.297 r_dihedral_angle_2_deg 13.055 r_long_range_B_refined 8.025 r_long_range_B_other 7.925 r_dihedral_angle_1_deg 7.153 r_scangle_other 6.076 r_mcangle_it 4.484 r_mcangle_other 4.482 r_scbond_it 4.028 r_scbond_other 4.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.297 r_dihedral_angle_2_deg 13.055 r_long_range_B_refined 8.025 r_long_range_B_other 7.925 r_dihedral_angle_1_deg 7.153 r_scangle_other 6.076 r_mcangle_it 4.484 r_mcangle_other 4.482 r_scbond_it 4.028 r_scbond_other 4.026 r_mcbond_it 3.161 r_mcbond_other 3.135 r_angle_refined_deg 1.758 r_angle_other_deg 0.597 r_chiral_restr 0.084 r_gen_planes_refined 0.01 r_bond_refined_d 0.001 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg 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 1915 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 20
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling PHASER phasing REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction