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Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand Gly-Pro-Arg-Pro-amide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LTJ PDB entry 1LTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 9% PEG 3350, 50 mM Tris-HCl pH 8.5, 2 mM Sodium azide, 12.5 mM Calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.17 61.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.009 α = 90 b = 95.009 β = 90 c = 448.382 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315 2005-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.99000 NSLS X29A
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 3.04 47.25 99.41 8 40798 61.8
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 PDB entry 1LTJ 3.04 47.25 38489 2030 99.41 0.23768 0.22049 0.2927 0.28802 0.329 RANDOM 61.947
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] 0.28 0.28 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_3_deg 17.123 r_dihedral_angle_4_deg 14.849 r_dihedral_angle_1_deg 5.648 r_angle_refined_deg 1.039 r_scangle_it 0.941 r_scbond_it 0.53 r_mcangle_it 0.516 r_nbtor_refined 0.301 r_mcbond_it 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_3_deg 17.123 r_dihedral_angle_4_deg 14.849 r_dihedral_angle_1_deg 5.648 r_angle_refined_deg 1.039 r_scangle_it 0.941 r_scbond_it 0.53 r_mcangle_it 0.516 r_nbtor_refined 0.301 r_mcbond_it 0.279 r_symmetry_hbond_refined 0.275 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.104 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 10657 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 80
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling