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Structure of the methyltransferase domain from Modoc Virus, a Flavivirus with No Known Vector (NKV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9K PDB ENTRY 1L9K
Crystallization Crystal Properties Matthews coefficient Solvent content 2.22 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.53 α = 90 b = 62.242 β = 90 c = 160.016 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 110 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.8 40 92 0.07 21.5 6.7 45634
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 1.8 1.9 63.7 0.32 4.1 4.6
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 PDB ENTRY 1L9K 1.8 40 43257 2318 91.98 0.18828 0.18586 0.1852 0.23479 0.2329 RANDOM 18.107
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] -0.22 0.15 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_4_deg 17.833 r_dihedral_angle_3_deg 14.711 r_dihedral_angle_1_deg 5.266 r_scangle_it 4.413 r_scbond_it 2.779 r_mcangle_it 1.581 r_angle_refined_deg 1.384 r_mcbond_it 1.118 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_4_deg 17.833 r_dihedral_angle_3_deg 14.711 r_dihedral_angle_1_deg 5.266 r_scangle_it 4.413 r_scbond_it 2.779 r_mcangle_it 1.581 r_angle_refined_deg 1.384 r_mcbond_it 1.118 r_nbtor_refined 0.304 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3777 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing