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Structure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) complexed with the molecular tweezer CLR01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2M ammonium citrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.752 α = 90 b = 148.752 β = 90 c = 189.957 γ = 120
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 2017-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97794 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.6 48.69 99.5 0.131 0.139 0.998 9.25 8.99 72820 80.073
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 97.8 2.249 2.397 0.603 0.97 8.321
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 48.69 70717 2101 99.48 0.232 0.2307 0.2284 0.2774 0.2702 RANDOM 86.127
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] 2.29 1.15 2.29 -7.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.466 r_dihedral_angle_3_deg 17.649 r_dihedral_angle_4_deg 16.288 r_dihedral_angle_1_deg 6.741 r_mcangle_it 2.408 r_mcbond_it 1.394 r_mcbond_other 1.394 r_angle_refined_deg 1.232 r_angle_other_deg 1.099 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.466 r_dihedral_angle_3_deg 17.649 r_dihedral_angle_4_deg 16.288 r_dihedral_angle_1_deg 6.741 r_mcangle_it 2.408 r_mcbond_it 1.394 r_mcbond_other 1.394 r_angle_refined_deg 1.232 r_angle_other_deg 1.099 r_chiral_restr 0.046 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16829 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing