☰ Navigation Tabs
Crystal structure of the third RCC1-like domain of HERC1
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, HANGING DROP 7.5 291 20% PEG 1500, 0.2 M Magnesium Choride, 0.1 M Hepes pH7.5, vapor diffusion hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.383 α = 70.93 b = 70.902 β = 81.26 c = 105.549 γ = 90.84
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 315r 2013-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 100 0.165 0.165 7.1 3.3 97126 97126 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 100 0.525 1.53 3.3 4850
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 50 97125 980 99.61 0.1817 0.1813 0.1888 0.2214 0.2273 RANDOM 19.6993
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] -0.97 -0.02 -0.15 0.59 0.19 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_4_deg 14.337 r_dihedral_angle_3_deg 11.782 r_dihedral_angle_1_deg 5.736 r_mcangle_it 1.626 r_angle_refined_deg 1.292 r_mcbond_it 0.988 r_mcbond_other 0.987 r_angle_other_deg 0.774 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_4_deg 14.337 r_dihedral_angle_3_deg 11.782 r_dihedral_angle_1_deg 5.736 r_mcangle_it 1.626 r_angle_refined_deg 1.292 r_mcbond_it 0.988 r_mcbond_other 0.987 r_angle_other_deg 0.774 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10636 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 33
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling Coot model building