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Structure of Gankyrin-S6ATPase photo-cross-linked site-specifically, and incoporated by genetic code expansion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVW PDB ENTRY 2DVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 31% polyethylene glycol 4000, 0.26M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.164 α = 90 b = 103.164 β = 90 c = 154.993 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 MX225HE 2008-12-15 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RAYONIX MX-225 2008-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU SPring-8 BL41XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 SPring-8 BL26B2
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 2.05 50 100 0.098 20.7 4.2 38604 26.5
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 2.05 2.18 99.9 0.454 3.2 4.2 6083
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2DVW 2.05 42.93 -3 38604 1914 100 0.171 0.171 0.1711 0.229 0.2288 RANDOM 37.4
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] 4.13 4.13 -8.27
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_angle_deg 2.8 c_improper_angle_d 1.78 c_bond_d 0.032 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_angle_deg 2.8 c_improper_angle_d 1.78 c_bond_d 0.032 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4668 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement DENZO data reduction SCALEPACK data scaling