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Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in complex with the reaction product succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 protein buffer: 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl and 2% (w/v) glycerol; precipitant solution: 29 % (w/v) PEG 2000-MME, soak with 20 mM sodium succinate for 1 hour
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.58 α = 90 b = 151.81 β = 90 c = 159.1 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2015-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 55 100 0.28 6.9 9.64 112964 36.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 99.8 1.32 9.82
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 2W8Q 2.2 50.07 112956 5648 100 0.189 0.188 0.2038 0.22 0.2355 RANDOM 37.11
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] -0.678 -1.7462 2.4242
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.96 t_omega_torsion 3.25 t_angle_deg 1.12 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.96 t_omega_torsion 3.25 t_angle_deg 1.12 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 14873 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 269
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing