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Caspase-6 in complex with Z-VAD-FMK inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WDP pdb entry 2wdp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.3 298 0.1 M lithium sulfate, 0.1 M sodium citrate, 11% 2-propanol , VAPOR DIFFUSION, temperature 298K, pH 4.3
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.206 α = 90 b = 65.446 β = 91.24 c = 91.718 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 2.65 29.1 99.2 0.114 14.8 7.5 30244 30002
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 2.65 2.79 98.8 0.564 3.6 7.6
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 (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 2wdp 2.65 29.1 28824 28380 1505 98.46 0.24275 0.24038 0.2388 0.28713 0.2862 RANDOM 24.792
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] 1.31 -0.02 -2.25 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.767 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 13.3 r_dihedral_angle_1_deg 5.004 r_scangle_it 0.857 r_angle_refined_deg 0.815 r_angle_other_deg 0.746 r_mcangle_it 0.657 r_scbond_it 0.528 r_mcbond_it 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.767 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 13.3 r_dihedral_angle_1_deg 5.004 r_scangle_it 0.857 r_angle_refined_deg 0.815 r_angle_other_deg 0.746 r_mcangle_it 0.657 r_scbond_it 0.528 r_mcbond_it 0.353 r_chiral_restr 0.049 r_mcbond_other 0.03 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6898 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling