7RKW

Naegleria fowleri CYP51(NfCYP51) complex with (S)-1-(4-fluorophenyl)-2-(1H-imidazol-1-yl)ethyl 3,5-dichlorobenzoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TL8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729630 mM Calcium chloride; 3.18% v/v Jefframine M-600 pH-7.0; 33% v/v Polyethylene glycol monomethyl ether 550; 100 mM Bis-Tris Propane pH-7.0
Crystal Properties
Matthews coefficientSolvent content
2.2244.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.29α = 90
b = 55.28β = 100.14
c = 72.06γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 6MMIRRORS2021-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1159ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8170.9493.70.000560.000620.99912.196.0694043155.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8658.70.03550.041340.1230.363.57

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 REPLACEMENTTHROUGHOUT5TL81.8170.9438337202093.460.19150.1890.24RANDOM60.927
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]
2.67-2.42-2.370.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.749
r_dihedral_angle_4_deg17.693
r_dihedral_angle_3_deg16.832
r_dihedral_angle_1_deg6.636
r_angle_refined_deg1.864
r_angle_other_deg1.594
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.749
r_dihedral_angle_4_deg17.693
r_dihedral_angle_3_deg16.832
r_dihedral_angle_1_deg6.636
r_angle_refined_deg1.864
r_angle_other_deg1.594
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3600
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing