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Crystal structure of stabilized human uPAR mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YWH PDB ENTRY 1YWH and 2FD6 experimental model PDB 2FD6 PDB ENTRY 1YWH and 2FD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 295 100 mM HEPES, pH 7.5, 2% (w/v) PEG400, 2 M ammonium sulfate, vapor diffusion, sitting drop, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.97 58.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.235 α = 90 b = 111.235 β = 90 c = 78.571 γ = 120
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 MARMOSAIC 300 mm CCD 2008-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.39 50 99.3 0.097 15.7 5.2 14133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 93.9 0.6 4.2
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 1YWH and 2FD6 2.39 33.04 14130 706 99 0.214 0.213 0.2127 0.252 0.2481 RANDOM 71.02
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] -1.61 -0.8 -1.61 2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.52 r_dihedral_angle_4_deg 23.551 r_dihedral_angle_3_deg 21.467 r_dihedral_angle_1_deg 8.477 r_angle_refined_deg 2.008 r_chiral_restr 0.134 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.52 r_dihedral_angle_4_deg 23.551 r_dihedral_angle_3_deg 21.467 r_dihedral_angle_1_deg 8.477 r_angle_refined_deg 2.008 r_chiral_restr 0.134 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2017 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 42
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing