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Ulilysin metalloprotease in complex with batimastat.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CKI PDB ENTRY 2CKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 VAPOUR-DIFFUSION CRYSTALLISATION METHOD FROM SITTING DROPS CONSISTING OF 1 MICROLITER OF PROULILYSIN (5 MG/ML IN 30MM TRIS-HCL PH 7.5, 2MM DITHIOTHREITOL, 100MM NACL), 1 MICROLITER OF RESERVOIR SOLUTION (18% PEG 8000, 0.1M 2-MORPHOLINOETHANESULFONIC ACID, PH6.5, 0.2M CACL2) AND, OPTIONALLY, 0.2 MICROLITER OF 0.1M SPERMIDINE OR 30% 2, 4-METHYLPENTANEDIOL AS ADDITIVES.
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.85 α = 90 b = 60.73 β = 90 c = 168.94 γ = 90
Symmetry Space Group C 2 2 21
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 45.6 97 0.04 24.2 3.8 154616 16
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 2.11 90.3 0.07 13.9 3.8
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 2CKI 2 50 39606 520 96.4 0.161 0.161 0.167 0.211 0.213 RANDOM 17
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] -1.25 3.05 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.003 r_dihedral_angle_4_deg 14.841 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 5.969 r_scangle_it 1.927 r_scbond_it 1.204 r_angle_refined_deg 1.181 r_mcangle_it 0.68 r_mcbond_it 0.384 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.003 r_dihedral_angle_4_deg 14.841 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 5.969 r_scangle_it 1.927 r_scbond_it 1.204 r_angle_refined_deg 1.181 r_mcangle_it 0.68 r_mcbond_it 0.384 r_nbtor_refined 0.301 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.172 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 4038 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling