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Structure of karilysin catalytic MMP domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MNC PDB ENTRY 1MNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 CRYSTALLIZATION ASSAYS WERE PERFORMED BY THE SITTING-DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTIONS WERE PREPARED BY A TECAN ROBOT AND CRYSTALLIZATION DROPS WERE DISPENSED ON 96X2-WELL MRC PLATES (INNOVADYNE) BY A CARTESIAN (GENOMIC SOLUTIONS) NANODROP ROBOT AT THE HIGH-THROUGHPUT CRYSTALLOGRAPHY PLATFORM AT BARCELONA SCIENCE PARK. CRYSTALS SUITABLE FOR STRUCTURE ANALYSIS WERE OBTAINED FOR UNBOUND KLY18 IN A BRUKER STEADY-TEMPERATURE CRYSTAL FARM AT 20C FROM DROPS CONTAINING 100NL OF PROTEIN SOLUTION (AT 9MG ML-1 IN 5MM TRIS-HCL, PH8.0, 0.02% SODIUM AZIDE) AND 100NL OF 45% 2-METHYL-2,4-PENTANEDIOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH8.5 AS RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.37 α = 90 b = 53.11 β = 134.55 c = 86.3 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.4 45.3 99.3 0.09 14.8 4.1 15411 38.4
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 2.53 95.9 0.51 2.5 3.4
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 1MNC 2.4 50 14703 708 99.28 0.19197 0.18877 0.1891 0.25872 0.2146 RANDOM 33.731
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] 3.2 2.49 -1.7 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.332 r_dihedral_angle_3_deg 17.064 r_dihedral_angle_4_deg 15.179 r_dihedral_angle_1_deg 6.729 r_scangle_it 2.264 r_scbond_it 1.46 r_angle_refined_deg 1.321 r_mcangle_it 1.109 r_angle_other_deg 0.886 r_mcbond_it 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.332 r_dihedral_angle_3_deg 17.064 r_dihedral_angle_4_deg 15.179 r_dihedral_angle_1_deg 6.729 r_scangle_it 2.264 r_scbond_it 1.46 r_angle_refined_deg 1.321 r_mcangle_it 1.109 r_angle_other_deg 0.886 r_mcbond_it 0.603 r_mcbond_other 0.106 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2702 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing