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X-Ray Structure of apo-EleNRMT in complex with two Nanobodies at 4.1A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QIA PDBID 7QIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 50 mM MgAc, 50 mM HEPES pH 7.2-7.6 and 25-30% PEG400
Crystal Properties Matthews coefficient Solvent content 2.75 55.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.27 α = 90 b = 122.25 β = 107.794 c = 149.11 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2021-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999869 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 4.1 12 99.2 0.112 0.999 15.36 28.2 25065 174.298
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.1 4.2 98.9 1.536 0.95 1.81 27.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDBID 7QIA 4.1 11.99 1.39 23739 1136 98.18 0.2693 0.2669 0.269 0.3155 0.3138 287.33
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9044 f_angle_d 0.6034 f_chiral_restr 0.043 f_plane_restr 0.0048 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9632 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX phasing PHENIX refinement XDS data reduction Coot model building XSCALE data scaling