6TIB

Structure of A. niger Fdc I327S variant in complex with 2 naphthoic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.642α = 90
b = 63.592β = 90
c = 87.741γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.0787.7495.60.15816.56.5169880
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)
11.071.1773.91.1270.71.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE4ZAA1.0787.74169880854372.0580.1260.12430.151912.67
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]
0.363-0.335-0.028
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.929
r_dihedral_angle_4_deg22.231
r_dihedral_angle_3_deg11.822
r_dihedral_angle_1_deg6.774
r_rigid_bond_restr5.293
r_scangle_it4.531
r_scangle_other4.53
r_scbond_other4.072
r_scbond_it4.071
r_lrange_it3.888
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.929
r_dihedral_angle_4_deg22.231
r_dihedral_angle_3_deg11.822
r_dihedral_angle_1_deg6.774
r_rigid_bond_restr5.293
r_scangle_it4.531
r_scangle_other4.53
r_scbond_other4.072
r_scbond_it4.071
r_lrange_it3.888
r_lrange_other3.443
r_angle_refined_deg2.148
r_mcangle_other2.122
r_mcangle_it2.09
r_mcbond_it2.046
r_mcbond_other1.968
r_angle_other_deg1.676
r_symmetry_nbd_refined0.33
r_nbd_other0.292
r_symmetry_xyhbond_nbd_refined0.29
r_nbd_refined0.265
r_xyhbond_nbd_refined0.229
r_symmetry_nbd_other0.205
r_nbtor_refined0.18
r_chiral_restr0.142
r_metal_ion_refined0.097
r_symmetry_nbtor_other0.088
r_gen_planes_refined0.023
r_bond_refined_d0.02
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3850
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling