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STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKR PDB ENTRY 1PKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 24% (W/V) PEG 8000, 0.1 M NA-HEPES, PH 7.0, 0.15 M LI2(SO4)
Crystal Properties Matthews coefficient Solvent content 2.51 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.43 α = 90 b = 79.2 β = 90 c = 30.78 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 123 IMAGE PLATE RIGAKU RAXIS II MSC-YALE MIRRORS 1997-04-19 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.66 35.26 72 0.042 0.051 14 2.5 16720 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.86 37 0.087 0.13 3.6 2.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1PKR 1.66 7 1 16720 15014 84 0.166 15.4
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 22.4 p_staggered_tor 17.8 p_planar_tor 5.2 p_multtor_nbd 0.24 p_xyhbond_nbd 0.23 p_singtor_nbd 0.18 p_chiral_restr 0.16 p_planar_d 0.05 p_angle_d 0.034 p_bond_d 0.016
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 22.4 p_staggered_tor 17.8 p_planar_tor 5.2 p_multtor_nbd 0.24 p_xyhbond_nbd 0.23 p_singtor_nbd 0.18 p_chiral_restr 0.16 p_planar_d 0.05 p_angle_d 0.034 p_bond_d 0.016 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1296 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms
Software Software Software Name Purpose RIGAKU data collection RIGAKU data reduction AMoRE phasing PROFFT refinement R-AXIS data reduction R-AXIS data scaling