6EV3

Structure of wild type A. niger Fdc1 that has been illuminated with UV light, with prFMN in the iminium and ketimine form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZA4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.448.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.131α = 90
b = 63.906β = 90
c = 87.853γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.364.8596.47.43.7475106
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3461.2230.51.13.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4ZA41.364.85121466629095.850.174240.173070.19711RANDOM14.446
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]
-0.510.76-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.553
r_dihedral_angle_4_deg20.76
r_dihedral_angle_3_deg11.892
r_long_range_B_refined11.122
r_long_range_B_other11.045
r_dihedral_angle_1_deg6.429
r_scangle_other2.981
r_angle_refined_deg2.244
r_scbond_other2.077
r_scbond_it2.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.553
r_dihedral_angle_4_deg20.76
r_dihedral_angle_3_deg11.892
r_long_range_B_refined11.122
r_long_range_B_other11.045
r_dihedral_angle_1_deg6.429
r_scangle_other2.981
r_angle_refined_deg2.244
r_scbond_other2.077
r_scbond_it2.076
r_mcangle_other1.833
r_mcangle_it1.83
r_mcbond_it1.288
r_mcbond_other1.288
r_angle_other_deg1.181
r_chiral_restr0.161
r_bond_refined_d0.023
r_gen_planes_refined0.015
r_gen_planes_other0.005
r_bond_other_d0.002
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 Atoms3852
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing