7AV4

Dark state structure of the C432S mutant of Fatty Acid Photodecarboxylase (FAP)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5277~ 20-30 % PEG 4000, 0.1 M Citrate pH5.5, 10 mM spermidine
Crystal Properties
Matthews coefficientSolvent content
3.1761.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.375α = 90
b = 104.683β = 90
c = 156.179γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.93686.95699.40.0970.99810.83.82163665692439.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9362.0598.10.5413.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6yru1.93646.73156924280999.380.1770.17520.2116random selection36.163
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]
2.656-0.799-1.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.346
r_dihedral_angle_4_deg16.633
r_dihedral_angle_3_deg14.367
r_dihedral_angle_1_deg7.696
r_lrange_it6.479
r_lrange_other6.437
r_scangle_it5.361
r_scangle_other5.361
r_scbond_it3.724
r_scbond_other3.724
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.346
r_dihedral_angle_4_deg16.633
r_dihedral_angle_3_deg14.367
r_dihedral_angle_1_deg7.696
r_lrange_it6.479
r_lrange_other6.437
r_scangle_it5.361
r_scangle_other5.361
r_scbond_it3.724
r_scbond_other3.724
r_mcangle_it3.447
r_mcangle_other3.443
r_mcbond_it2.607
r_mcbond_other2.602
r_angle_refined_deg1.649
r_angle_other_deg1.381
r_nbd_other0.205
r_nbd_refined0.201
r_symmetry_nbd_other0.181
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.161
r_symmetry_nbd_refined0.148
r_symmetry_xyhbond_nbd_refined0.126
r_symmetry_nbtor_other0.081
r_chiral_restr0.075
r_symmetry_xyhbond_nbd_other0.014
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4234
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing