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Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA)
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 66.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.529 α = 90 b = 64.529 β = 90 c = 157.033 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 PILATUS 6M 2016-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979290 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.4 59.69 100 0.157 0.033 22.2 23.9 5025
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.67 100 0.578 0.116 8.5 25.2 989
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 3.4 59.69 4739 246 99.94 0.18301 0.18113 0.185 0.21585 0.2108 RANDOM 86.054
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] 6.58 6.58 -13.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.924 r_dihedral_angle_4_deg 23.406 r_dihedral_angle_3_deg 14.241 r_long_range_B_refined 8.085 r_long_range_B_other 8.083 r_scangle_other 6.029 r_dihedral_angle_1_deg 6.003 r_mcangle_it 4.965 r_mcangle_other 4.963 r_scbond_it 3.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.924 r_dihedral_angle_4_deg 23.406 r_dihedral_angle_3_deg 14.241 r_long_range_B_refined 8.085 r_long_range_B_other 8.083 r_scangle_other 6.029 r_dihedral_angle_1_deg 6.003 r_mcangle_it 4.965 r_mcangle_other 4.963 r_scbond_it 3.599 r_scbond_other 3.597 r_mcbond_it 2.973 r_mcbond_other 2.973 r_angle_refined_deg 1.223 r_angle_other_deg 0.944 r_chiral_restr 0.068 r_bond_refined_d 0.007 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 126 Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling