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Second PDZ domain of Ligand of Numb protein X 2 by Laue crystallography (no electric field)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SSRL structure at 277 K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 27-31% PEG 300, 48 mM citric acid, 35 mM NaH2PO4
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.3 α = 90 b = 39.45 β = 117.54 c = 39.01 γ = 90
Symmetry Space Group C 1 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 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 1.8 50 79.3 0.096 19.6 9.8 6565 2 11.49
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 34.7 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SSRL structure at 277 K (to be deposited) 1.8 30.1 0.28 6565 328 78.88 0.1325 0.1316 0.1419 0.1483 0.1458 PHENIX default
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 13.172 f_angle_d 1.63 f_chiral_restr 0.102 f_bond_d 0.02 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 719 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Precognition data reduction Epinorm data reduction PHENIX phasing