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Zinc-mediated allosteric inhibiton of caspase-6
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, SITTING DROP 4.6 298 0.1 M Sodium Acetate pH 4.6, 2M NaCl, 3% EtOH, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.8 31.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.696 α = 90 b = 90.855 β = 90.3 c = 85.763 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 210 2012-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.2861 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.85 40 99.6 0.13 7.2 22532 3.8 6.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 61.8
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 2.85 30 22532 21332 1126 84.24 0.21591 0.21503 0.3018 0.2329 0.32 RANDOM 29.647
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] 16.76 -0.12 -19.32 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.38 r_dihedral_angle_3_deg 18.98 r_dihedral_angle_4_deg 16.342 r_dihedral_angle_1_deg 6.315 r_angle_refined_deg 0.737 r_mcangle_it 0.233 r_scangle_it 0.148 r_mcbond_it 0.129 r_scbond_it 0.086 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.38 r_dihedral_angle_3_deg 18.98 r_dihedral_angle_4_deg 16.342 r_dihedral_angle_1_deg 6.315 r_angle_refined_deg 0.737 r_mcangle_it 0.233 r_scangle_it 0.148 r_mcbond_it 0.129 r_scbond_it 0.086 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6764 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling