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Structure of Nrd1 RNA binding domain in complex with RNA (UUAGUAAUCC)
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 66.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.157 α = 90 b = 66.157 β = 90 c = 156.908 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 S 6M 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.53 60.96 99.5 0.081 0.99 9.7 9.7 4716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.53 3.87 99.1 0.435 0.99 2.4 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.53 60.96 4432 238 99.43 0.2273 0.22512 0.2357 0.26861 0.2761 RANDOM 122.488
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] 8.5 8.5 -17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.207 r_dihedral_angle_4_deg 16.147 r_dihedral_angle_3_deg 14.855 r_long_range_B_other 10.324 r_long_range_B_refined 10.317 r_scangle_other 7.262 r_mcangle_other 7.008 r_mcangle_it 6.999 r_dihedral_angle_1_deg 6.297 r_scbond_it 4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.207 r_dihedral_angle_4_deg 16.147 r_dihedral_angle_3_deg 14.855 r_long_range_B_other 10.324 r_long_range_B_refined 10.317 r_scangle_other 7.262 r_mcangle_other 7.008 r_mcangle_it 6.999 r_dihedral_angle_1_deg 6.297 r_scbond_it 4.28 r_mcbond_it 4.272 r_scbond_other 4.269 r_mcbond_other 4.129 r_angle_refined_deg 1.158 r_angle_other_deg 0.943 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 1303 Nucleic Acid Atoms 134 Solvent Atoms 2 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction Aimless data scaling Coot model building