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Structure of M-calpain in complex with Calpastatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KFU PDB ENTRY 1KFU PDB ENTRY 1TL9 experimental model PDB 1TL9 PDB ENTRY 1KFU PDB ENTRY 1TL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 pH 6.5, microbatch under paraffin oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.477 α = 90 b = 66.985 β = 100.76 c = 108.656 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 MIRRORS 2007-04-24 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 66.965 96.7 0.084 0.084 7.7 3.6 36208 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 82.5 0.317 0.317 2.2 3.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KFU PDB ENTRY 1TL9 2.4 66.23 34375 1819 96.47 0.20062 0.19756 0.25784 0.2416 RANDOM 11.827
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] 0.48 -0.33 0.22 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.765 r_dihedral_angle_3_deg 17.628 r_dihedral_angle_4_deg 13.445 r_dihedral_angle_1_deg 6.138 r_scangle_it 1.919 r_angle_refined_deg 1.237 r_scbond_it 1.166 r_mcangle_it 0.841 r_mcbond_it 0.51 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.765 r_dihedral_angle_3_deg 17.628 r_dihedral_angle_4_deg 13.445 r_dihedral_angle_1_deg 6.138 r_scangle_it 1.919 r_angle_refined_deg 1.237 r_scbond_it 1.166 r_mcangle_it 0.841 r_mcbond_it 0.51 r_nbtor_refined 0.299 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.122 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.086 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_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 7396 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction