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Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in complex with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MZ5
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, 1 mM NADP+; precipitant solution: 35% (w/v) PEG 2000-MME
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.38 α = 90 b = 165.28 β = 90 c = 138.38 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 6M 2017-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9786 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.3 50 99.5 0.099 0.999 15.1 12.9 91956 68.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.43 97.6 0.772 1 12.8
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 5MZ5 2.3 46.13 91565 4579 99.9 0.185 0.183 0.2005 0.207 0.2222 RANDOM 83.67
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] 12.868 -1.2507 -11.6173
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.51 t_omega_torsion 2.98 t_angle_deg 1.1 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 18.51 t_omega_torsion 2.98 t_angle_deg 1.1 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 14866 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 204
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing