☰ Navigation Tabs
Crystal structure of PDE6D bound to HRas peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M Tris pH 8.5, 8% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.626 α = 90 b = 82.789 β = 90 c = 112.467 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 56.234 99.8 1 16.9 6.4 24377
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.772
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5TB5 1.95 56.234 24329 1197 99.75 0.233 0.2295 0.2343 0.2993 0.3021 41.591
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] -0.543 2.041 -1.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.034 r_dihedral_angle_3_deg 17.526 r_dihedral_angle_4_deg 15.96 r_lrange_it 7.551 r_lrange_other 7.547 r_dihedral_angle_1_deg 7.101 r_scangle_it 5.633 r_scangle_other 5.631 r_mcangle_it 4.318 r_mcangle_other 4.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.034 r_dihedral_angle_3_deg 17.526 r_dihedral_angle_4_deg 15.96 r_lrange_it 7.551 r_lrange_other 7.547 r_dihedral_angle_1_deg 7.101 r_scangle_it 5.633 r_scangle_other 5.631 r_mcangle_it 4.318 r_mcangle_other 4.316 r_scbond_it 3.822 r_scbond_other 3.821 r_mcbond_it 3.359 r_mcbond_other 3.359 r_angle_other_deg 1.538 r_angle_refined_deg 1.165 r_symmetry_nbd_other 0.222 r_nbd_other 0.212 r_nbd_refined 0.181 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.144 r_ncsr_local_group_1 0.138 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.04 r_xyhbond_nbd_other 0.039 r_symmetry_xyhbond_nbd_other 0.01 r_bond_other_d 0.003 r_bond_refined_d 0.002 r_gen_planes_refined 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2440 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing