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Crystal structure of human sarcomeric mitochondrial creatine kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 17% PEG-3350, 10mM DTT, 0.2M diammonium citrate, 0.1M Bis-TRIS, protein buffer also contained magnesium chloride, creatine, ADP
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.057 α = 70.12 b = 106.058 β = 84.57 c = 114.932 γ = 68.61
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 2006-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00003 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 49.09 95.4 0.077 0.077 0.995 8.5 2 247985
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 95.5 0.897 0.894 0.318 1 2 12346
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 THROUGHOUT 2GL6 2.1 40 214294 4357 95.4 0.203 0.2023 0.2362 0.2153 THIN SHELLS (SFTOOLS) 38.291
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] -0.6 0.37 -0.84 -0.14 -0.49 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.673 r_dihedral_angle_4_deg 16.369 r_dihedral_angle_3_deg 12.095 r_dihedral_angle_1_deg 5.749 r_mcangle_it 3.829 r_mcbond_it 2.49 r_mcbond_other 2.49 r_angle_refined_deg 1.267 r_angle_other_deg 0.903 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.673 r_dihedral_angle_4_deg 16.369 r_dihedral_angle_3_deg 12.095 r_dihedral_angle_1_deg 5.749 r_mcangle_it 3.829 r_mcbond_it 2.49 r_mcbond_other 2.49 r_angle_refined_deg 1.267 r_angle_other_deg 0.903 r_chiral_restr 0.069 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21843 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 306
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling