☰ Navigation Tabs
A WRPW peptide bound to the Groucho-TLE WD40 domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GXR PDB ENTRY 1GXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 287 6MG/ML PROTEIN WAS MIXED 1:1 WITH 12% PEG8000, 100MM NACACODYLATE PH6.5, 100MM NAACETATE AT 14C IN MICROBATCH. PEPTIDES WERE ADDED TO THE PROTEIN CRYSTALS IN 125 MM NACL, 25 MM TRIS PH8.0, 0.5 MM EDTA TO A FINAL CONCENTRATION OF 0.76 MM, AND INCUBATED FOR 16 H BEFORE HARVESTING AND WASHING IN 50MM NA CACODYLATE PH6.5, 12 % PEG 8K, AND CRYO-PROTECTED IN 30% ETHYLENE GLYCOL 50MM NA CACODYLATE PH6.5, 12 % PEG 8K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.81 α = 90 b = 56.478 β = 112.68 c = 126.642 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2005-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.12 45 97.5 0.06 13.4 3.4 78005
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 2.12 2.24 83 0.25 4.6 2.9
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 1GXR 2.12 117.04 74067 3924 97.7 0.181 0.178 0.1773 0.244 0.2402 RANDOM 25.93
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] -0.98 -0.65 0.15 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.092 r_dihedral_angle_4_deg 20.019 r_dihedral_angle_3_deg 15.151 r_dihedral_angle_1_deg 8.636 r_scangle_it 3.857 r_scbond_it 2.677 r_angle_refined_deg 2.012 r_mcangle_it 1.845 r_mcbond_it 1.137 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.092 r_dihedral_angle_4_deg 20.019 r_dihedral_angle_3_deg 15.151 r_dihedral_angle_1_deg 8.636 r_scangle_it 3.857 r_scbond_it 2.677 r_angle_refined_deg 2.012 r_mcangle_it 1.845 r_mcbond_it 1.137 r_nbtor_refined 0.309 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.238 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.135 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10424 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing