☰ Navigation Tabs
The second PDZ domain of Ligand of Numb protein X 2 in the presence of an electric field of ~1 MV/cm along the crystallographic x axis, with eightfold extrapolation of structure factor differences.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E11
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 27-31% PEG-300, 43 mM citric acid, 35 mM NaH2PO4
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.146 α = 113.31 b = 38.146 β = 113.31 c = 39.01 γ = 62.28
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289 CCD RAYONIX MX340-HS U23 and U27; KB mirror system. 2015-03-20 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.02-1.16 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.797 28.95 70.18 0.0765 6.98 5.2 11291
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.797 1.861 17.78 0.67
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 FREE R-VALUE 5E11 1.797 28.95 10873 1089 67.59 0.2914 0.289 0.3046 0.3127 0.3169 RANDOM
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 16.967 f_angle_d 1.803 f_chiral_restr 0.094 f_bond_d 0.018 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1425 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement Precognition data reduction Epinorm data reduction PHENIX phasing