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Crystal Structure of DAD2 in complex with 2-(2-methyl-3-nitroanilino)benzoic acid
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 8.5 291 Tris/Acetate 0.1M, MgCl2 0.2M, PEG 3350 27%
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.697 α = 82.67 b = 48.315 β = 86.76 c = 71.942 γ = 69.95
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 2015-08-06 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 1.51 45.08 95.9 0.084 0.098 0.049 0.998 12.1 4 69577 10.3
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 1.51 1.53 74.9 0.83 0.966 0.492 0.593 3.7
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 1.51 36.27 66090 3485 95.87 0.1661 0.1644 0.1762 0.1973 0.2075 RANDOM 19.047
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] -0.1 0.12 -0.09 -0.01 0.2 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.059 r_dihedral_angle_4_deg 15.842 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_1_deg 5.677 r_angle_refined_deg 1.76 r_angle_other_deg 1.436 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.059 r_dihedral_angle_4_deg 15.842 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_1_deg 5.677 r_angle_refined_deg 1.76 r_angle_other_deg 1.436 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.01 r_bond_other_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4154 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 46
Software Software Software Name Purpose XDS data scaling Aimless data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction