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The X-ray Crystal Structure of Full-Length type II Human Plasminogen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QRZ 1QRZ, 1KRN, 5HPG, 1LOS experimental model PDB 1KRN 1QRZ, 1KRN, 5HPG, 1LOS experimental model PDB 5HPG 1QRZ, 1KRN, 5HPG, 1LOS experimental model PDB 1LOS 1QRZ, 1KRN, 5HPG, 1LOS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 0.1M sodium citrate, 0.2M sodium acetate, polyethylene glycol 1000, polyethylene glycol 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.98 69.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.62 α = 90 b = 144.62 β = 90 c = 233.67 γ = 120
Symmetry Space Group P 32 2 1
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 315r Silicon mirrors (adaptive and U-bent) 2011-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953692 Australian Synchrotron MX2
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 2.45 125.25 99.8 0.175 0.071 9.2 6.9 104073 3 3 43.58
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 2.45 2.58 98.9 0.855 0.351 2.3 5.4 79752
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 1QRZ, 1KRN, 5HPG, 1LOS 2.45 125.25 104035 5236 99.8 0.191 0.1897 0.2003 0.2155 0.2289 RANDOM 34.1888
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] -2.7801 -2.7801 5.5603
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.54 t_omega_torsion 2.07 t_angle_deg 0.96 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.54 t_omega_torsion 2.07 t_angle_deg 0.96 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11671 Nucleic Acid Atoms Solvent Atoms 1436 Heterogen Atoms 111
Software Software Software Name Purpose ADSC data collection PHASES phasing BUSTER refinement XDS data reduction SCALA data scaling