☰ Navigation Tabs
Catalytic Domain of Human Calpain-9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 20% PEG 3350, 0.2 M Ammonium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.308 α = 90 b = 80.9 β = 90 c = 100.545 γ = 90
Symmetry Space Group P 2 2 21
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 MARRESEARCH 2005-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID APS 32-ID
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 2.31 19.83 99.7 0.069 19.2 3.7 16773 -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) 2.31 2.43 100 0.34 3.4 3.7
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 1MDW 2.31 19.38 15919 850 99.71 0.20684 0.20345 0.2038 0.27165 0.2756 RANDOM 45.306
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] -0.38 1.58 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.714 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_3_deg 16.703 r_dihedral_angle_1_deg 6.69 r_scangle_it 5.362 r_scbond_it 3.704 r_mcangle_it 3.107 r_mcbond_it 1.978 r_angle_refined_deg 1.413 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.714 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_3_deg 16.703 r_dihedral_angle_1_deg 6.69 r_scangle_it 5.362 r_scbond_it 3.704 r_mcangle_it 3.107 r_mcbond_it 1.978 r_angle_refined_deg 1.413 r_nbtor_refined 0.308 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.214 r_symmetry_vdw_refined 0.177 r_metal_ion_refined 0.115 r_chiral_restr 0.105 r_symmetry_hbond_refined 0.065 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 2465 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing