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The crystal structure of uPA complex with peptide inhibitor MH027 at pH4.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NWN PDB ENTRY 2NWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.05M SODIUM CITRATE, 1.95M (NH4)2SO4, 0.05% NAN3, 5% PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.317 α = 90 b = 121.317 β = 90 c = 43.457 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 325 mm CCD 2010-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.58 60 84.8 0.074 0.09 17.7 4.7 36480 30708
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 1.58 1.62 91 0.53 0.538 1.17 2.8 1764
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 2NWN 1.58 40.16 30708 1619 98.9 0.20653 0.20529 0.2034 0.2302 0.2262 RANDOM 21.408
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] -0.38 -0.19 -0.38 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.957 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_4_deg 13.472 r_dihedral_angle_1_deg 6.115 r_scangle_it 2.641 r_scbond_it 1.606 r_mcangle_it 1.195 r_angle_refined_deg 1.089 r_mcbond_it 0.616 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.957 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_4_deg 13.472 r_dihedral_angle_1_deg 6.115 r_scangle_it 2.641 r_scbond_it 1.606 r_mcangle_it 1.195 r_angle_refined_deg 1.089 r_mcbond_it 0.616 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2041 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling