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Structure of karilysin MMP-like catalytic domain in complex with inhibitory tetrapeptide SWFP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Best crystals were obtained at 20 degrees from 1:1 microL drops with complex solution (8mg/mL in 5mM Tris HCl pH8, 5mM calcium chloride, 0.02% sodium azide) and 0.4M sodium/potassium tartrate as reservoir solution. Crystals were cryo-protected by immersion in cryo-solution (0.32M sodium/potassium tartrate, 25%[v/v] glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.05 α = 90 b = 86.05 β = 90 c = 49.44 γ = 90
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 ADSC QUANTUM 315r 2011-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 1.55 42.9 99.9 0.081 18.4 7 26370 26344 2 21.2
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 1.55 1.59 98.7 0.749 2.1 4.3
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 FOURIER SYNTHESIS THROUGHOUT 2XS4 1.55 42.87 26370 26318 1335 99.9 0.1465 0.1465 0.1453 0.1475 0.171 0.1513 RANDOM 17.58
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] 0.5945 0.5945 -1.1891
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.18 t_other_torsion 2.7 t_angle_deg 0.92 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.18 t_other_torsion 2.7 t_angle_deg 0.92 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1333 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 34
Software Software Software Name Purpose ADSC data collection BUSTER refinement XDS data reduction XSCALE data scaling