6EV9

Structure of E277D A. niger Fdc1 with prFMN in the hydroxylated 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
2.3748.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.91α = 90
b = 63.46β = 90
c = 87.72γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.987DiamondI03

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
11.6464.73997.214.465903
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.6991.2954.4

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 REPLACEMENTTHROUGHOUT4ZA41.6464.7362666323699.430.167670.165780.20494RANDOM17.411
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]
-0.620.95-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.823
r_dihedral_angle_4_deg20.744
r_dihedral_angle_3_deg12.511
r_dihedral_angle_1_deg6.55
r_long_range_B_refined4.77
r_long_range_B_other4.77
r_scangle_other2.819
r_scbond_other1.898
r_scbond_it1.897
r_angle_refined_deg1.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.823
r_dihedral_angle_4_deg20.744
r_dihedral_angle_3_deg12.511
r_dihedral_angle_1_deg6.55
r_long_range_B_refined4.77
r_long_range_B_other4.77
r_scangle_other2.819
r_scbond_other1.898
r_scbond_it1.897
r_angle_refined_deg1.896
r_mcangle_it1.833
r_mcangle_other1.833
r_mcbond_it1.305
r_mcbond_other1.303
r_angle_other_deg1.082
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.003
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 Atoms3814
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing