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Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-amide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LT9 PDB ENTRY 1LT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 50 mM Tris, 12.5 mM calcium chloride, 12% PEG 3350, 2 mM sodium azide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.476 α = 90 b = 146.596 β = 90 c = 228.96 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2005-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97625 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 50 83 29.5 6.7 82662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.28 80.5 0.284 3.4 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1LT9 2.3 49.21 100841 78322 4129 99.74 0.21573 0.21436 0.2116 0.24154 0.2385 RANDOM 33.558
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] 0.18 1.12 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_4_deg 14.968 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_1_deg 5.663 r_scangle_it 1.741 r_scbond_it 1.1 r_angle_refined_deg 1.079 r_mcangle_it 0.975 r_mcbond_it 0.549 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_4_deg 14.968 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_1_deg 5.663 r_scangle_it 1.741 r_scbond_it 1.1 r_angle_refined_deg 1.079 r_mcangle_it 0.975 r_mcbond_it 0.549 r_nbtor_refined 0.299 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.104 r_metal_ion_refined 0.087 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10371 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 data collection