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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 0.1M 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 BL17U 0.9793 SSRF BL17U
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 99.7 0.096 2.03 3.6 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 4 0.096
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 0.233 0.2306 0.2322 0.2786 0.2752 RANDOM 40.382
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] 0.47 0.73 -2.59 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.247 r_dihedral_angle_4_deg 21.034 r_dihedral_angle_3_deg 18.385 r_dihedral_angle_1_deg 7.347 r_angle_refined_deg 1.624 r_angle_other_deg 1.199 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.247 r_dihedral_angle_4_deg 21.034 r_dihedral_angle_3_deg 18.385 r_dihedral_angle_1_deg 7.347 r_angle_refined_deg 1.624 r_angle_other_deg 1.199 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6526 Nucleic Acid Atoms 1327 Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASER phasing