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Crystal structure of spRlmCD with U747 stemloop RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Ammonium acetate, 0.1M sodium acetate, pH5.2, 20%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.23 α = 74.58 b = 62.259 β = 85.47 c = 79.818 γ = 65.03
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 2017-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9774 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.18 56.37 87.8 0.13 0.152 0.078 0.991 6.2 3.7 48209
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.29 67.9 0.551 0.647 0.338 0.891 3.5
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 5XJ1 2.18 56.37 45786 2293 87.53 0.248 0.2454 0.2478 0.3033 0.3064 RANDOM 39.567
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.904 r_dihedral_angle_4_deg 22.899 r_dihedral_angle_3_deg 18.887 r_dihedral_angle_1_deg 7.834 r_angle_refined_deg 1.318 r_angle_other_deg 0.862 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.904 r_dihedral_angle_4_deg 22.899 r_dihedral_angle_3_deg 18.887 r_dihedral_angle_1_deg 7.834 r_angle_refined_deg 1.318 r_angle_other_deg 0.862 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6978 Nucleic Acid Atoms 516 Solvent Atoms 67 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing