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Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RI1 PDB entry 1RI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 20% PEG 3350, 0.2 M KCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.787 α = 90 b = 99.672 β = 90 c = 167.782 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 CCD ADSC QUANTUM 315 2007-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792996 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 50 99.9 0.141 27.9 17.6 58716 58716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 99.7 0.698 3.35 14.8 5774
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1RI1 2.3 49.51 55206 55206 2942 98.92 0.22486 0.22486 0.22122 0.29448 0.2705 RANDOM 34.903
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] 3.6 -2.43 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.527 r_dihedral_angle_4_deg 21.954 r_dihedral_angle_3_deg 17.133 r_dihedral_angle_1_deg 6.936 r_scangle_it 3.825 r_scbond_it 2.57 r_mcangle_it 1.798 r_angle_refined_deg 1.697 r_mcbond_it 1.074 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.527 r_dihedral_angle_4_deg 21.954 r_dihedral_angle_3_deg 17.133 r_dihedral_angle_1_deg 6.936 r_scangle_it 3.825 r_scbond_it 2.57 r_mcangle_it 1.798 r_angle_refined_deg 1.697 r_mcbond_it 1.074 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.153 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8779 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing