4ZA4

Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Initial screening of 0.3 microl 14 mg/ml A. niger Fdc1 in 100 mM NaCl, 25 mM Tris pH 7.5 and 0.3 microl reservoir solution at 4C resulted in a number of hits including PACT condition F4 (molecular dimensions). Seed stock produced from these crystals was used in an optimization screen based around 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350 mixing 0.05 microl seed stock, 0.25 microl protein solution and 0.3 microl reservoir solution at 4C.
Crystal Properties
Matthews coefficientSolvent content
2.3948.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.99α = 90
b = 63.93β = 90
c = 87.63γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.987DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.2233.8299.960.03711.26.1152260
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.221.2599.990.35425.8

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 REPLACEMENTTHROUGHOUT1.2233.82152260804199.960.146520.145730.16111RANDOM9.809
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]
1.04-2.271.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.569
r_dihedral_angle_4_deg21.066
r_dihedral_angle_3_deg12.311
r_mcbond_other7.517
r_dihedral_angle_1_deg6.603
r_scangle_it6.569
r_rigid_bond_restr5.09
r_scbond_it4.873
r_angle_other_deg4.393
r_mcangle_it3.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.569
r_dihedral_angle_4_deg21.066
r_dihedral_angle_3_deg12.311
r_mcbond_other7.517
r_dihedral_angle_1_deg6.603
r_scangle_it6.569
r_rigid_bond_restr5.09
r_scbond_it4.873
r_angle_other_deg4.393
r_mcangle_it3.096
r_angle_refined_deg2.384
r_mcbond_it2.338
r_chiral_restr0.158
r_bond_refined_d0.028
r_gen_planes_other0.02
r_gen_planes_refined0.018
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 Atoms3847
Nucleic Acid Atoms
Solvent Atoms447
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing