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Catalytic domain of Human Calpain-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TLO PDB ENTRY 1TLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.75 298 1.5 M Ammononium Formate, 0.1 M Tris pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.75
Crystal Properties Matthews coefficient Solvent content 3.39 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.534 α = 90 b = 90.534 β = 90 c = 433.102 γ = 120
Symmetry Space Group P 61 2 2
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 SBC-3 2005-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 44.32 98.9 0.089 20.56 8.4 42153 -3
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) 2.4 2.49 94.6 0.569 1.44 3.1
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 1TLO 2.4 44.32 41996 39890 2106 98.83 0.22174 0.21955 0.2192 0.26387 0.2625 RANDOM 44.488
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] 1.8 0.9 1.8 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 15.726 r_dihedral_angle_1_deg 5.75 r_scangle_it 3.871 r_scbond_it 2.571 r_mcangle_it 2.351 r_mcbond_it 1.404 r_angle_refined_deg 1.127 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 15.726 r_dihedral_angle_1_deg 5.75 r_scangle_it 3.871 r_scbond_it 2.571 r_mcangle_it 2.351 r_mcbond_it 1.404 r_angle_refined_deg 1.127 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.25 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.132 r_metal_ion_refined 0.129 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_other r_symmetry_vdw_other 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 5142 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing