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RVD HA specifically contacts 5mC through van der Waals interactions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 8-10% PEG3350 (w/v), 10% ethanol, and 0.1 M MES pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.786 α = 90 b = 88.022 β = 104.77 c = 89.349 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 100 CCD MAR CCD 130 mm 2017-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.48 86.4 98.8 0.096 2.03 3.5 39755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.52 0.908
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 4GJP 2.48 86.4 39755 2095 91.79 0.2259 0.2233 0.2249 0.2752 0.2717 RANDOM 44.467
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] 0.03 0.18 -1.11 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.857 r_dihedral_angle_3_deg 19.558 r_dihedral_angle_4_deg 19.281 r_dihedral_angle_1_deg 9.644 r_angle_refined_deg 1.717 r_angle_other_deg 1.405 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.857 r_dihedral_angle_3_deg 19.558 r_dihedral_angle_4_deg 19.281 r_dihedral_angle_1_deg 9.644 r_angle_refined_deg 1.717 r_angle_other_deg 1.405 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7215 Nucleic Acid Atoms 1382 Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing