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Crystal structure of VACV D13 in complex with Rifaximin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SAM pdbid 3SAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 298 3.5-4.0 M sodium formate and 0.1 M citric acid
Crystal Properties Matthews coefficient Solvent content 3.59 65.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.14 α = 90 b = 191.14 β = 90 c = 253.27 γ = 120
Symmetry Space Group P 61 2 2
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 210 2013-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 3.11 20 99.9 0.33 0.337 0.994 12.96 22.118 49697 -3 75.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.19 98.6 2.044 2.092 0.647 1.89 22.08
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 pdbid 3SAM 3.11 20 49339 2455 100 0.198 0.197 0.201 0.218 0.2162 RANDOM 56.32
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] 4.3445 4.3445 -8.6889
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.18 t_omega_torsion 2.11 t_angle_deg 0.95 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.18 t_omega_torsion 2.11 t_angle_deg 0.95 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12668 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 88
Software Software Software Name Purpose XSCALE data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Coot model building BUSTER phasing