8RKQ

Structure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) complexed with the molecular tweezer CLR01


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V9G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2M ammonium citrate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4449.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.752α = 90
b = 148.752β = 90
c = 189.957γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97794SLSX10SA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.648.6999.50.1310.1390.9989.258.997282080.073
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)RedundancyNumber Unique Reflections (All)
12.62.6797.82.2492.3970.6030.978.321

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.648.6970717210199.480.2320.23070.2774RANDOM86.127
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]
2.291.152.29-7.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.466
r_dihedral_angle_3_deg17.649
r_dihedral_angle_4_deg16.288
r_dihedral_angle_1_deg6.741
r_mcangle_it2.408
r_mcbond_it1.394
r_mcbond_other1.394
r_angle_refined_deg1.232
r_angle_other_deg1.099
r_chiral_restr0.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.466
r_dihedral_angle_3_deg17.649
r_dihedral_angle_4_deg16.288
r_dihedral_angle_1_deg6.741
r_mcangle_it2.408
r_mcbond_it1.394
r_mcbond_other1.394
r_angle_refined_deg1.232
r_angle_other_deg1.099
r_chiral_restr0.046
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16829
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing