8HFJ

Crystal Structure of CbAR mutant (H162F) in complex with NADP+ and a bulky 1,3-cyclodiketone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910.1 M HEPES pH 7.5, 15% isopropanol and 19% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1743.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.92α = 90
b = 124.92β = 90
c = 133.778γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2022-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.7524.1199.80.9837.96.826700
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.8460.23

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 REPLACEMENTTHROUGHOUT7YB12.7524.1126700138399.720.208060.20480.27012RANDOM19.907
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]
0.670.67-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.081
r_dihedral_angle_4_deg18.765
r_dihedral_angle_3_deg17.222
r_dihedral_angle_1_deg8.338
r_long_range_B_refined4.202
r_long_range_B_other4.202
r_scangle_other2.289
r_mcangle_it2.162
r_mcangle_other2.162
r_angle_refined_deg1.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.081
r_dihedral_angle_4_deg18.765
r_dihedral_angle_3_deg17.222
r_dihedral_angle_1_deg8.338
r_long_range_B_refined4.202
r_long_range_B_other4.202
r_scangle_other2.289
r_mcangle_it2.162
r_mcangle_other2.162
r_angle_refined_deg1.654
r_scbond_other1.369
r_scbond_it1.367
r_mcbond_it1.299
r_mcbond_other1.299
r_angle_other_deg1.268
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms7659
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms224

Software

Software
Software NamePurpose
SAINTdata scaling
REFMACrefinement
SAINTdata reduction
MOLREPphasing