4ZA7

Structure of A. niger Fdc1 in complex with alpha-methyl cinnamic acid


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.448.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.94α = 90
b = 64.17β = 90
c = 87.73γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9DiamondI03

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
11.187.7980.03511.24.2203456
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.11.1397.82.42.7

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 REPLACEMENTTHROUGHOUT4ZA41.130.052034561057999.980.132610.13220.14048RANDOM10.253
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]
1.04-2.221.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.751
r_dihedral_angle_4_deg20.896
r_dihedral_angle_3_deg12.126
r_scangle_it6.784
r_dihedral_angle_1_deg6.346
r_scbond_it5.081
r_mcangle_it3.259
r_rigid_bond_restr2.805
r_angle_refined_deg2.469
r_mcbond_it2.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.751
r_dihedral_angle_4_deg20.896
r_dihedral_angle_3_deg12.126
r_scangle_it6.784
r_dihedral_angle_1_deg6.346
r_scbond_it5.081
r_mcangle_it3.259
r_rigid_bond_restr2.805
r_angle_refined_deg2.469
r_mcbond_it2.441
r_mcbond_other2.421
r_angle_other_deg1.774
r_chiral_restr0.198
r_bond_refined_d0.028
r_gen_planes_refined0.018
r_gen_planes_other0.013
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_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 Atoms3844
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing