4ZA9

Structure of A. niger fdc1 in complex with a phenylpyruvate derived adduct to the prenylated flavin cofactor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.05α = 90
b = 63.85β = 90
c = 87.68γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.0163.8599.970.02714.34264342
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.011.0499.990.3142.22.2

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 DIFFRACTIONTHROUGHOUT1.0163.852643421389399.970.130640.12990.14501RANDOM9.383
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]
0.96-1.971.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.731
r_dihedral_angle_4_deg20.328
r_dihedral_angle_3_deg11.4
r_mcbond_other6.899
r_dihedral_angle_1_deg6.408
r_scangle_it5.787
r_rigid_bond_restr4.631
r_angle_other_deg4.353
r_scbond_it4.309
r_mcangle_it2.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.731
r_dihedral_angle_4_deg20.328
r_dihedral_angle_3_deg11.4
r_mcbond_other6.899
r_dihedral_angle_1_deg6.408
r_scangle_it5.787
r_rigid_bond_restr4.631
r_angle_other_deg4.353
r_scbond_it4.309
r_mcangle_it2.715
r_angle_refined_deg2.25
r_mcbond_it1.98
r_chiral_restr0.198
r_bond_refined_d0.029
r_gen_planes_refined0.026
r_gen_planes_other0.023
r_bond_other_d
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3807
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing