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Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M TrisHCl pH 7, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.12 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.198 α = 90 b = 120.441 β = 102.73 c = 67.778 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 80 CCD ADSC QUANTUM 315 2014-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9793 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 3 50 99.9 0.135 6.2 3.6 14580
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 0.843
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 50 13397 743 99.52 0.24972 0.24702 0.259 0.29668 0.3081 RANDOM 86.628
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] 12.98 -1.51 -7.29 -4.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.139 r_dihedral_angle_3_deg 16.447 r_long_range_B_refined 15.648 r_long_range_B_other 15.648 r_dihedral_angle_4_deg 13.532 r_scangle_other 9.855 r_mcangle_other 8.876 r_mcangle_it 8.875 r_scbond_it 6.024 r_scbond_other 6.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.139 r_dihedral_angle_3_deg 16.447 r_long_range_B_refined 15.648 r_long_range_B_other 15.648 r_dihedral_angle_4_deg 13.532 r_scangle_other 9.855 r_mcangle_other 8.876 r_mcangle_it 8.875 r_scbond_it 6.024 r_scbond_other 6.021 r_dihedral_angle_1_deg 5.879 r_mcbond_it 5.581 r_mcbond_other 5.569 r_angle_refined_deg 1.361 r_angle_other_deg 1.268 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4573 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASER phasing