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Structure of Nrd1 RNA binding domain in complex with RNA (GUAA)
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 1M Sodium Potassium Phosphate pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.936 α = 90 b = 64.936 β = 90 c = 158.391 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 PIXEL DECTRIS PILATUS3 6M 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979490 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 2.45 60.08 96.1 0.04 0.1 1 28.2 16.7 12717
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 2.45 2.55 0.63 0.154 0.97 3.4 17.7
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 5O1W 2.45 60.08 12040 621 96.16 0.1977 0.19668 0.2027 0.21724 0.2179 RANDOM 61.307
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] 2.05 2.05 -4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.302 r_dihedral_angle_4_deg 20.254 r_dihedral_angle_3_deg 15.418 r_long_range_B_other 9.268 r_long_range_B_refined 9.265 r_scangle_other 6.522 r_dihedral_angle_1_deg 6.155 r_mcangle_it 5.549 r_mcangle_other 5.546 r_scbond_it 3.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.302 r_dihedral_angle_4_deg 20.254 r_dihedral_angle_3_deg 15.418 r_long_range_B_other 9.268 r_long_range_B_refined 9.265 r_scangle_other 6.522 r_dihedral_angle_1_deg 6.155 r_mcangle_it 5.549 r_mcangle_other 5.546 r_scbond_it 3.916 r_scbond_other 3.914 r_mcbond_it 3.41 r_mcbond_other 3.409 r_angle_refined_deg 1.364 r_angle_other_deg 0.974 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 1310 Nucleic Acid Atoms 84 Solvent Atoms 38 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building MOLREP phasing