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Calcium-dependent complex between m-calpain and calpastatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDW PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI experimental model PDB 1DF0 PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI experimental model PDB 1DVI PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 4-9% PEG 3350, 5-10 mM CaCl2, 50-100 mM NaOAc (pH 5.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.29 46.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.39 α = 90 b = 147.39 β = 90 c = 47.222 γ = 90
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 2007-07-02 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH 4 1 x-ray 100 CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH 1,2,3,4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.98064 ALS 5.0.3 2 SYNCHROTRON NSLS BEAMLINE X29A 0.98064 NSLS X29A 3 SYNCHROTRON APS BEAMLINE 22-ID 0.98064 APS 22-ID 4 SYNCHROTRON APS BEAMLINE 22-BM 0.98064 APS 22-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 1,2,3,4 2.95 49.25 0.096 21.4 4.4 20755 2 92
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) 1,2,3,4 2.95 3.06 0.82 2.1 4.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI 2.95 49.15 20755 1164 99.83 0.232 0.229 0.223 0.299 0.3008 RANDOM 94.719
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] -0.62 -0.62 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.977 r_dihedral_angle_3_deg 22.028 r_angle_other_deg 16.358 r_dihedral_angle_4_deg 15.986 r_dihedral_angle_1_deg 7.187 r_scangle_it 1.975 r_angle_refined_deg 1.485 r_scbond_it 1.208 r_mcangle_it 0.904 r_mcbond_it 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.977 r_dihedral_angle_3_deg 22.028 r_angle_other_deg 16.358 r_dihedral_angle_4_deg 15.986 r_dihedral_angle_1_deg 7.187 r_scangle_it 1.975 r_angle_refined_deg 1.485 r_scbond_it 1.208 r_mcangle_it 0.904 r_mcbond_it 0.53 r_symmetry_hbond_refined 0.345 r_nbtor_other 0.32 r_nbtor_refined 0.318 r_nbd_other 0.313 r_nbd_refined 0.252 r_xyhbond_nbd_refined 0.179 r_metal_ion_refined 0.172 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.108 r_mcbond_other 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7290 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection