8PNS | pdb_00008pns

Crystal structure of the acyl-CoA dehydrogenase PA0506 (FadE1) from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62940.1M MES pH6, 0.1M Calcium chloride dihydrate, 20% w/v PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.6653.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.918α = 90
b = 155.918β = 90
c = 99.511γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2021-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9179DiamondI04-1

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
12.08135.031000.2380.2460.0610.9968.215.98248726.61
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)
12.082.1299.172.93.0410.9050.370.411.12

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.08135.0378359405999.920.206170.203920.21590.248720.2541RANDOM40.223
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]
0.680.340.68-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.175
r_dihedral_angle_4_deg18.236
r_dihedral_angle_3_deg17.062
r_long_range_B_refined7.61
r_long_range_B_other7.608
r_dihedral_angle_1_deg6.755
r_scangle_other6.093
r_mcangle_it4.558
r_mcangle_other4.557
r_scbond_it4.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.175
r_dihedral_angle_4_deg18.236
r_dihedral_angle_3_deg17.062
r_long_range_B_refined7.61
r_long_range_B_other7.608
r_dihedral_angle_1_deg6.755
r_scangle_other6.093
r_mcangle_it4.558
r_mcangle_other4.557
r_scbond_it4.142
r_scbond_other4.142
r_mcbond_it3.242
r_mcbond_other3.242
r_angle_refined_deg1.699
r_angle_other_deg1.336
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9141
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms234

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction