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Crystal structure of DAD2 D166A 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 8.5 293 0.1 M Trizma-acetate-bicine (pH 8.5), 0.06 M divalents (MgCl2 and CaCl2), 45-55% PEG 500 MME PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.08 40.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.69 α = 94.47 b = 56.53 β = 94.67 c = 68.04 γ = 108.83
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 210r 2018-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.52 30.33 95.1 0.089 0.104 0.052 0.997 7.8 3.9 75017
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 1.52 1.55 93.2 0.669 0.775 0.39 0.721 3.9
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 1.52 30.33 71299 3718 95.07 0.1724 0.171 0.1842 0.1991 0.2111 RANDOM 17.78
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] 0.61 -0.13 0.1 -0.82 1.46 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.229 r_dihedral_angle_4_deg 17.607 r_dihedral_angle_3_deg 12.544 r_dihedral_angle_1_deg 6.427 r_angle_refined_deg 1.513 r_angle_other_deg 1.479 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.229 r_dihedral_angle_4_deg 17.607 r_dihedral_angle_3_deg 12.544 r_dihedral_angle_1_deg 6.427 r_angle_refined_deg 1.513 r_angle_other_deg 1.479 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4150 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 13
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction