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Structure of the two tandem Tudor domains and a new identified KH0 domain from human Fragile X Mental Retardation Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.15 76.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.643 α = 90 b = 60.842 β = 122.99 c = 168.856 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 130 CCD ADSC QUANTUM 270 2013-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 50 99 39030 38927 3 3
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 3 3.05 99.9 2.4 7 1920
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3O8V 3 50 38644 36716 1928 95.82 0.2207 0.2187 0.2183 0.2586 0.2554 RANDOM 99
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] -0.79 -5.76 7.98 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.3 r_dihedral_angle_3_deg 20.143 r_dihedral_angle_4_deg 19.961 r_long_range_B_other 15.106 r_long_range_B_refined 15.104 r_mcangle_it 10.031 r_mcangle_other 10.03 r_scangle_other 9.966 r_dihedral_angle_1_deg 7.1 r_mcbond_it 6.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.3 r_dihedral_angle_3_deg 20.143 r_dihedral_angle_4_deg 19.961 r_long_range_B_other 15.106 r_long_range_B_refined 15.104 r_mcangle_it 10.031 r_mcangle_other 10.03 r_scangle_other 9.966 r_dihedral_angle_1_deg 7.1 r_mcbond_it 6.206 r_mcbond_other 6.197 r_scbond_it 6.085 r_scbond_other 6.084 r_angle_refined_deg 1.358 r_angle_other_deg 0.796 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6229 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 16
Software Software Software Name Purpose ADSC data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling