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Crystal structure of DAD2 N242I mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M MES pH 6.5
1.58-1.72 M MgSO4
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.736 α = 90 b = 133.736 β = 90 c = 99.764 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953736 Australian Synchrotron MX2
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 1.58 45.86 100 0.088 0.09 0.021 1 20.3 19.1 138411
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 1.58 1.61 100 2.188 2.248 0.517 0.728 18.9
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 4DNP 1.58 45.81 128380 9970 99.99 0.1399 0.138 0.1384 0.1649 0.1652 RANDOM 26.861
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] 1.48 0.74 1.48 -4.81
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.638 r_dihedral_angle_2_deg 26.711 r_sphericity_bonded 25.257 r_dihedral_angle_4_deg 21.06 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_1_deg 5.835 r_rigid_bond_restr 3.782 r_angle_refined_deg 1.74 r_angle_other_deg 1.569 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.638 r_dihedral_angle_2_deg 26.711 r_sphericity_bonded 25.257 r_dihedral_angle_4_deg 21.06 r_dihedral_angle_3_deg 11.974 r_dihedral_angle_1_deg 5.835 r_rigid_bond_restr 3.782 r_angle_refined_deg 1.74 r_angle_other_deg 1.569 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4142 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 58
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction