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Crystal structure of the extended Tudor domain from BmPAPI in complex with sDMA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 0.95 M ammonium sulfate, 50 mM sodium acetate, pH 5.5 and 5% glucose.
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.03 α = 90 b = 66.03 β = 90 c = 224.48 γ = 90
Symmetry Space Group P 43 21 2
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 2015-06-25 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 2.4 39.61 92.8 0.077 8.7 3.7 18600
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 2.4 2.51 95 0.535 1.6 3 6867
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5VQG 2.4 39.61 17693 878 91.1 0.198 0.195 0.262 0.2462 RANDOM 45.17
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] -0.36 -0.36 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.697 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 15.052 r_long_range_B_refined 8.179 r_long_range_B_other 8.177 r_dihedral_angle_1_deg 6.949 r_scangle_other 5.839 r_mcangle_it 4.773 r_mcangle_other 4.772 r_scbond_it 3.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.697 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 15.052 r_long_range_B_refined 8.179 r_long_range_B_other 8.177 r_dihedral_angle_1_deg 6.949 r_scangle_other 5.839 r_mcangle_it 4.773 r_mcangle_other 4.772 r_scbond_it 3.611 r_scbond_other 3.603 r_mcbond_it 3.108 r_mcbond_other 3.106 r_angle_refined_deg 1.482 r_angle_other_deg 0.774 r_chiral_restr 0.079 r_bond_refined_d 0.012 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 3213 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction XDS data scaling PHASER phasing