8VRE

Structure of PYCR1 complexed with NADH and N-formyl-L-proline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XP3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Reservoir contained 340 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 4 mM N-formyl-L-proline (resuspended in DMSO). The final DMSO concentration was 4%. Crystal was soaked in cryobuffer containing 20% PEG 200 and 25 mM N-formyl-L-proline (resuspended in DMSO). The final DMSO concentration in the cryobuffer was 25%
Crystal Properties
Matthews coefficientSolvent content
2.550.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.529α = 90
b = 179.294β = 106.8
c = 88.36γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8391.1398.20.070.0810.0410.99810.83.8267999
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)RedundancyNumber Unique Reflections (All)
11.831.8699.10.8821.0220.510.5723.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.8371.50.312679991313593.510.17630.1750.2015
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.79
f_angle_d1.003
f_chiral_restr0.057
f_plane_restr0.009
f_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9795
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms280

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing