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Crystal structure of the free aminoterminal fragment of urokinase type plasminogen activator (ATF)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URK PDB ENTRY 1URK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 293 1.2 M sodium dihydrogen phosphate, 0.8 M potassium hydrogen phosphate, 200 mM lithium sulfate, 100 mM CHES, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.603 α = 107.62 b = 64.327 β = 92.11 c = 64.623 γ = 95.75
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 225 mm 2005-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.13539 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 40 96.4 0.045 19.63 3.8 54650 54650 -3
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 1.9 1.97 87 0.221 2.58 2.8 4899
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 1URK 1.9 15 51775 2757 96.14 0.1829 0.18153 0.1811 0.20822 0.2082 RANDOM 29.676
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] 0.17 0.6 -0.75 0.02 -0.46 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.287 r_dihedral_angle_4_deg 16.955 r_dihedral_angle_3_deg 13.186 r_dihedral_angle_1_deg 6.336 r_scangle_it 3.81 r_scbond_it 2.534 r_mcangle_it 1.544 r_angle_refined_deg 1.489 r_mcbond_it 0.945 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.287 r_dihedral_angle_4_deg 16.955 r_dihedral_angle_3_deg 13.186 r_dihedral_angle_1_deg 6.336 r_scangle_it 3.81 r_scbond_it 2.534 r_mcangle_it 1.544 r_angle_refined_deg 1.489 r_mcbond_it 0.945 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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_refined 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 3897 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing