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Crystal structure of uPA in complex with a camelid-derived antibody fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 289 Sodium Phosphate dibasic, Ammonium Sulfate, MES, Tween 20
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.985 α = 90 b = 77.749 β = 102.4 c = 61.454 γ = 90
Symmetry Space Group C 1 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 110 CCD ADSC QUANTUM 315 2015-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.97 30 97.4 0.058 0.067 0.032 8.4 4.2 59384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2 92.6 0.364 0.421 0.21 0.89 3.7 2804
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.97 30 56384 2999 97.37 0.1688 0.1673 0.1772 0.1964 0.2074 RANDOM 31.205
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] -0.39 -0.47 0.24 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.119 r_dihedral_angle_4_deg 16.295 r_dihedral_angle_3_deg 13.043 r_dihedral_angle_1_deg 6.614 r_mcangle_it 2.462 r_mcbond_it 1.665 r_mcbond_other 1.664 r_angle_refined_deg 1.6 r_angle_other_deg 1.241 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.119 r_dihedral_angle_4_deg 16.295 r_dihedral_angle_3_deg 13.043 r_dihedral_angle_1_deg 6.614 r_mcangle_it 2.462 r_mcbond_it 1.665 r_mcbond_other 1.664 r_angle_refined_deg 1.6 r_angle_other_deg 1.241 r_chiral_restr 0.129 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5783 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 127
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing