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Crystal structure of mRNA cap guanine-N7 methyltransferase (RNMT) in complex with sinefungin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 20% PEG 3350, 0.2 M KSCN, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.515 α = 90 b = 73.65 β = 90 c = 147.518 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2008-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 40 97.2 0.094 15.874 4.8 24532
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 96 0.39 4.6 2381
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 (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 2.41 38.92 24501 1260 96.95 0.231 0.228 0.2258 0.3 0.2956 RANDOM 31.856
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] -3.29 3.87 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.926 r_dihedral_angle_4_deg 21.375 r_dihedral_angle_3_deg 15.682 r_dihedral_angle_1_deg 6.642 r_scangle_it 2.621 r_scbond_it 1.825 r_angle_refined_deg 1.564 r_mcangle_it 1.067 r_mcbond_it 0.654 r_symmetry_hbond_refined 0.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.926 r_dihedral_angle_4_deg 21.375 r_dihedral_angle_3_deg 15.682 r_dihedral_angle_1_deg 6.642 r_scangle_it 2.621 r_scbond_it 1.825 r_angle_refined_deg 1.564 r_mcangle_it 1.067 r_mcbond_it 0.654 r_symmetry_hbond_refined 0.572 r_nbtor_refined 0.304 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4192 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 54
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOLREP phasing