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Crystal structure of a homohexameric MCM from M. acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R7Y Polyalanine model of the C-terminal ATPase domain of chain A. Loops were also removed from the model.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.03 M NPS, 0.1 M MOPS/HEPES pH 7.5, 10 % (w/v) PEG 20,000, 20 % (v/v) PEG MME 550
Crystal Properties Matthews coefficient Solvent content 3.24 61.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.699 α = 90 b = 127.488 β = 91.713 c = 177.038 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER2 XE 16M 2020-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.59 57.15 99.9 0.106 0.115 0.044 0.998 11.3 6.8 157088 64.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.64 98.2 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.59 57.15 1.33 154138 1983 98.02 0.2311 0.2309 0.232 0.2533 0.2537 96.45
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.8752 f_angle_d 1.4906 f_chiral_restr 0.0976 f_bond_d 0.0182 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26927 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 176
Software Software Software Name Purpose X-Area data reduction DIALS data scaling PHASER phasing Coot model building BUCCANEER model building PHENIX model building PHENIX refinement