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Structure of the first RCC1-like domain of HERC2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KCI pdb entry 3KCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291 1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.86 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.159 α = 90 b = 94.159 β = 90 c = 281.894 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 315 2013-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-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 2.6 93.965 100 0.14 13.8 10.7 45698 45698
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 100 0.011 1.084 0.7 11.1 6560
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 pdb entry 3KCI 2.6 40 45629 2500 99.893 0.201 0.1988 0.2083 0.2376 0.2426 thin shells (sftools) 49.761
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] 1.11 1.11 1.11 -3.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.874 r_dihedral_angle_3_deg 12.317 r_dihedral_angle_4_deg 11.208 r_dihedral_angle_1_deg 6.064 r_mcangle_it 2.398 r_mcbond_it 1.474 r_mcbond_other 1.473 r_angle_refined_deg 1.289 r_angle_other_deg 0.918 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.874 r_dihedral_angle_3_deg 12.317 r_dihedral_angle_4_deg 11.208 r_dihedral_angle_1_deg 6.064 r_mcangle_it 2.398 r_mcbond_it 1.474 r_mcbond_other 1.473 r_angle_refined_deg 1.289 r_angle_other_deg 0.918 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7783 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 89
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction