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The crystal structure of uPA complex with peptide inhibitor MH036 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, SITTING DROP 7.4 298 0.05M SODIUM CITRATE, 1.95M (NH4)2SO4, 0.05% NAN3, 5% PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.091 α = 90 b = 121.091 β = 90 c = 43.332 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 225 mm CCD 2010-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
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 2.31 60 99.8 0.051 0.043 52.7 3.8 10379 10358
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 2.31 2.35 100 0.06 0.054 41.5 3.5 515
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 2.31 40.05 9877 498 99.76 0.18526 0.18141 0.1802 0.26262 0.2541 RANDOM 15.639
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] -0.54 -0.27 -0.54 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_4_deg 12.629 r_dihedral_angle_1_deg 6.32 r_scangle_it 2.381 r_scbond_it 1.374 r_angle_refined_deg 1.217 r_mcangle_it 1.102 r_mcbond_it 0.577 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_4_deg 12.629 r_dihedral_angle_1_deg 6.32 r_scangle_it 2.381 r_scbond_it 1.374 r_angle_refined_deg 1.217 r_mcangle_it 1.102 r_mcbond_it 0.577 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2069 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling