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Structure of aldehyde dehydrogenase 12 (ALDH12) from Zea mays
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 50% v/v of a precipitant mixture containing 25% v/v 2-methyl-2,4-pentanediol, 25% w/v polyethylene glycol 1000, and 25% w/v polyethylene glycol 3350; and 0.1 M Tris/bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.05 40.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.642 α = 90 b = 123.737 β = 105.62 c = 103.707 γ = 90
Symmetry Space Group C 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 100 CMOS RDI CMOS_8M 2016-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1 ALS 4.2.2
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 2.2 61.87 99.3 0.092 0.109 0.057 0.996 11.6 3.5 98196 32.5
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 2.2 2.24 93.4 1.007 1.241 0.712 0.456 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4MPY 2.2 46.68 1.36 98146 4909 99.21 0.1668 0.1646 0.1658 0.21 0.2101 36.7229
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.485 f_angle_d 0.676 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16100 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 108
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction BALBES phasing