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Crystal structure of the extended Tudor domain from BmPAPI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 1% PEG 8,000, 50 mM MES, pH 5.5, 100 mM KCl and 10 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.56 α = 90 b = 63.56 β = 90 c = 100.74 γ = 120
Symmetry Space Group P 32 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 100 IMAGE PLATE RIGAKU 2015-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.6 31.78 99.5 0.106 7.8 4.1 7535
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 2.6 2.72 100 0.608 1.6 4
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 3FDR 2.6 31.78 7150 419 98.98 0.20571 0.20141 0.2053 0.27705 0.2828 RANDOM 34.595
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] -0.06 -0.03 -0.06 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.308 r_dihedral_angle_4_deg 17.659 r_dihedral_angle_3_deg 14.837 r_dihedral_angle_1_deg 6.741 r_long_range_B_refined 6.502 r_long_range_B_other 6.464 r_scangle_other 4.032 r_mcangle_it 3.873 r_mcangle_other 3.872 r_scbond_it 2.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.308 r_dihedral_angle_4_deg 17.659 r_dihedral_angle_3_deg 14.837 r_dihedral_angle_1_deg 6.741 r_long_range_B_refined 6.502 r_long_range_B_other 6.464 r_scangle_other 4.032 r_mcangle_it 3.873 r_mcangle_other 3.872 r_scbond_it 2.408 r_scbond_other 2.407 r_mcbond_it 2.324 r_mcbond_other 2.315 r_angle_refined_deg 1.416 r_angle_other_deg 0.777 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 1573 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction XDS data scaling PHENIX phasing