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Crystal structure containing UGGAA/UGGAA motif interacting with NCD molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.01 M Magnesium acetate tetrahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.5, 1.3 M Lithium sulfate monohydrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.628 α = 90 b = 71.628 β = 90 c = 62.879 γ = 90
Symmetry Space Group P 41 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-F 2020-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 47.3 100 1 24.64 25.7 26778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 0.89
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.501 47.299 26778 899 99.989 0.129 0.1282 0.1403 0.1661 0.1735 25.961
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] 0.38 0.38 -0.76
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 9.586 r_lrange_other 4.423 r_lrange_it 4.422 r_mcangle_it 3.451 r_scangle_it 3.2 r_scangle_other 3.199 r_angle_other_deg 3.082 r_scbond_it 2.761 r_scbond_other 2.76 r_mcbond_other 2.542
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 9.586 r_lrange_other 4.423 r_lrange_it 4.422 r_mcangle_it 3.451 r_scangle_it 3.2 r_scangle_other 3.199 r_angle_other_deg 3.082 r_scbond_it 2.761 r_scbond_other 2.76 r_mcbond_other 2.542 r_angle_refined_deg 1.616 r_nbtor_refined 0.259 r_symmetry_nbd_other 0.236 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.167 r_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.116 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.079 r_gen_planes_other 0.027 r_gen_planes_refined 0.02 r_bond_refined_d 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 602 Solvent Atoms 198 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing