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Catalytic Domain of Human Calpain 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ARY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 2M NH4PO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.19 61.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.794 α = 90 b = 91.794 β = 90 c = 194.592 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2006-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.2 50 96.3 0.119 7.1 4.7 47063 45317 37.9
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 2.28 98.6 0.812 4.5
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 2ARY 2.2 38.954 43796 2229 93.282 0.2048 0.2048 0.2048 0.21 0.2678 0.2682 RANDOM 17.801
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] 0.01 0.005 0.01 -0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.932 r_dihedral_angle_1_deg 23.819 r_dihedral_angle_3_deg 14.694 r_dihedral_angle_4_deg 13.809 r_scangle_it 2.309 r_scbond_it 1.548 r_angle_refined_deg 1.456 r_scangle_other 1.124 r_mcangle_it 1.104 r_angle_other_deg 1.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.932 r_dihedral_angle_1_deg 23.819 r_dihedral_angle_3_deg 14.694 r_dihedral_angle_4_deg 13.809 r_scangle_it 2.309 r_scbond_it 1.548 r_angle_refined_deg 1.456 r_scangle_other 1.124 r_mcangle_it 1.104 r_angle_other_deg 1.066 r_mcbond_it 0.711 r_mcangle_other 0.528 r_scbond_other 0.507 r_symmetry_vdw_refined 0.298 r_symmetry_vdw_other 0.247 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.207 r_nbd_other 0.189 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.171 r_mcbond_other 0.137 r_chiral_restr 0.124 r_metal_ion_refined 0.085 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5073 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling