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Structure of Nrd1 RNA binding domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 12% PEG 8000, 0.1 M Bicine pH 9
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.991 α = 90 b = 60.991 β = 90 c = 157.958 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 2M 2015-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.976250 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 48.14 99.1 32.1 24.5 13708 383024
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 SAD THROUGHOUT 2.3 56.9 13317 698 99.96 0.20796 0.2068 0.2097 0.23297 0.2416 RANDOM 59.946
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] 2.14 2.14 -4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.786 r_dihedral_angle_4_deg 22.598 r_dihedral_angle_3_deg 13.334 r_long_range_B_refined 7.906 r_long_range_B_other 7.906 r_dihedral_angle_1_deg 6.816 r_scangle_other 3.573 r_mcangle_it 2.909 r_mcangle_other 2.908 r_scbond_it 2.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.786 r_dihedral_angle_4_deg 22.598 r_dihedral_angle_3_deg 13.334 r_long_range_B_refined 7.906 r_long_range_B_other 7.906 r_dihedral_angle_1_deg 6.816 r_scangle_other 3.573 r_mcangle_it 2.909 r_mcangle_other 2.908 r_scbond_it 2.144 r_scbond_other 2.132 r_mcbond_it 1.761 r_mcbond_other 1.761 r_angle_refined_deg 1.306 r_angle_other_deg 0.906 r_chiral_restr 0.078 r_bond_refined_d 0.01 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 1327 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building XDS data scaling SHELX phasing