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Crystal Structure of Human Kallikrein 5 in complex with Leupeptin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDG PDB ENTRY 2BDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 30% PEG-monomethyl ether, 200 mM ammomium sulfate, 100 mM MES,10 mM leupeptin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.27 62.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.219 α = 90 b = 67.284 β = 94.35 c = 39.916 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 100 CCD MAR CCD 165 mm mirrors 2006-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.0500 MPG/DESY, HAMBURG BW6
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 2.3 20 99.7 0.083 21.8 5.7 14740 14701 1 26.2
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 2.3 2.34 94.8 0.202 6.4 694
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2BDG 2.3 19.9 14701 14047 709 95 0.244 0.221 0.221 0.2253 0.269 0.2622 RANDOM 51.5
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] -8.4 -0.79 32.22 -23.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 3.23 c_mcangle_it 2.73 c_scbond_it 2.18 c_mcbond_it 1.6 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1793 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 28
Software Software Software Name Purpose CNS refinement LABVIEW data collection DENZO data reduction SCALEPACK data scaling PHASER phasing