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Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with GlcNAc ligand bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M7H pdbid 4M7H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.5 M Ammonium Sulphate, 7% Dioxane, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.6 α = 90 b = 113.6 β = 90 c = 44.08 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2011-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.93 56.86 98.7 0.073 0.086 0.044 0.997 12.4 3.5 42095
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 1.93 1.98 98.5 0.379 0.453 0.243 0.796 3.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdbid 4M7H 1.93 56.8 40018 2077 98.38 0.1683 0.1671 0.1783 0.1912 0.2014 RANDOM 18.312
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] 0.61 0.61 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.237 r_dihedral_angle_4_deg 16.816 r_dihedral_angle_3_deg 12.959 r_dihedral_angle_1_deg 7.373 r_angle_refined_deg 1.409 r_angle_other_deg 1.346 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.237 r_dihedral_angle_4_deg 16.816 r_dihedral_angle_3_deg 12.959 r_dihedral_angle_1_deg 7.373 r_angle_refined_deg 1.409 r_angle_other_deg 1.346 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3520 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 97
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction