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Crystal structure of human MCM8/9 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DP3 7DP3, 7DPD experimental model PDB 7DPD 7DP3, 7DPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1M Bis-Tris propone, pH 6.0-7.5, 0.6M sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.616 α = 90 b = 185.616 β = 90 c = 185.616 γ = 90
Symmetry Space Group P 21 3
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 315 2015-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 6.6 41.5 97.81 0.061 0.99 39.8 13.7 4153 431.51
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 6.6 6.71 100 0.768 4.1 14.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7DP3, 7DPD 6.6 41.5 1.34 4104 415 98.37 0.3287 0.3209 0.3228 0.3977 0.3991 627.19
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 13.4456 f_angle_d 0.5135 f_chiral_restr 0.0405 f_plane_restr 0.0029 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8833 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose Coot model building PHENIX refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing