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Structure of Nrd1 RNA binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.2 M Potassium Thiocyanate, 23% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.39 α = 90 b = 58.39 β = 90 c = 92.446 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M KB focusing mirrors 2015-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979300 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.6 92.45 100 0.081 0.018 0.99 26.82 2 23596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.6 0.136 0.95 6.1 1197
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 5O1W 1.6 50.57 22455 1141 100 0.17904 0.17758 0.20805 0.2191 RANDOM 20.902
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] 0.29 0.14 0.29 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.341 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 11.753 r_dihedral_angle_1_deg 5.826 r_long_range_B_refined 4.688 r_long_range_B_other 4.387 r_scangle_other 1.966 r_mcangle_other 1.88 r_mcangle_it 1.879 r_angle_refined_deg 1.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.341 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 11.753 r_dihedral_angle_1_deg 5.826 r_long_range_B_refined 4.688 r_long_range_B_other 4.387 r_scangle_other 1.966 r_mcangle_other 1.88 r_mcangle_it 1.879 r_angle_refined_deg 1.249 r_scbond_it 1.168 r_scbond_other 1.157 r_mcbond_it 1.073 r_mcbond_other 1.058 r_angle_other_deg 0.891 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1303 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building XDS data scaling MOLREP phasing