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Crystal structure of calpain-3 penta-EF-hand domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ALV pdb entry 1ALV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 10% PEG 8000, 8% 1,2-ethanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.08 40.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107 α = 90 b = 107 β = 90 c = 96.71 γ = 90
Symmetry Space Group P 41 21 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 MARMOSAIC 300 mm CCD 2012-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9 APS 23-ID-B
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 2.45 47.852 100 0.137 18.01 14.4 21278 21268 -3 59.027
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 2.45 2.51 100 1.668 2.19
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR-SAD THROUGHOUT pdb entry 1ALV 2.45 47.85 21268 21219 1098 99.97 0.2019 0.1981 0.2687 0.2602 RANDOM 59.138
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.523 r_dihedral_angle_4_deg 22.82 r_dihedral_angle_3_deg 18.017 r_dihedral_angle_1_deg 6.636 r_mcangle_it 4.035 r_mcbond_other 2.566 r_mcbond_it 2.565 r_angle_refined_deg 1.518 r_angle_other_deg 0.853 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.523 r_dihedral_angle_4_deg 22.82 r_dihedral_angle_3_deg 18.017 r_dihedral_angle_1_deg 6.636 r_mcangle_it 4.035 r_mcbond_other 2.566 r_mcbond_it 2.565 r_angle_refined_deg 1.518 r_angle_other_deg 0.853 r_chiral_restr 0.085 r_bond_refined_d 0.012 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 4005 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 46
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction