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Mopeia Virus Exonuclease domain fully depleted of Manganese un ALD compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.1 M MES 25 % (M/W) PEG 8000) 3mM Mn
Crystal Properties Matthews coefficient Solvent content 2.56 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.853 α = 90 b = 38.29 β = 92.63 c = 137.315 γ = 90
Symmetry Space Group P 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93.15 PIXEL DECTRIS PILATUS 6M Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal 2018-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.08 137.17 99.6 0.121 0.135 0.058 0.996 10.6 5.3 28863 37.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.2 99.4 0.993 1.096 0.455 0.942 5.4
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 6SX8 2.08 68.58 28859 1346 99.5 0.25 0.248 0.2555 0.283 0.2823 RANDOM 53.84
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] -33.0693 10.9709 7.4012 25.6681
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.11 t_omega_torsion 3.42 t_angle_deg 1.03 t_bond_d 0.01 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 17.11 t_omega_torsion 3.42 t_angle_deg 1.03 t_bond_d 0.01 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 3183 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 2
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing