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Crystal structure of an active MCM hexamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VL6 SsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z) experimental model PDB 4R7Z SsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 281 10.8 mg/mL Sso-PfMCM; 5 mM ADP mixed 1:1 with 100 mM HEPES, pH 7.6; 350 mM MgCl2; 3 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.93 57.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.902 α = 90 b = 118.902 β = 90 c = 199.317 γ = 120
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 RAYONIX MX300HS 2014-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 50 99.8 0.107 14.8 6.8 43407 43329 -3 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 98.3 0.75 1.79 5 4313
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 SsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z) 2.7 49.83 39044 1976 89.7 0.263 0.263 0.2627 0.295 0.2952 RANDOM 61.3
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] -2.32 -2.32 4.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 2.75 c_mcangle_it 2.6 c_scbond_it 1.73 c_angle_deg 1.5 c_mcbond_it 1.46 c_improper_angle_d 1.1 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 2.75 c_mcangle_it 2.6 c_scbond_it 1.73 c_angle_deg 1.5 c_mcbond_it 1.46 c_improper_angle_d 1.1 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9430 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling