7RKR

Naegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(4-fluorophenyl)-2-(1H-imidazol-1-yl)ethyl 3-(trifluoromethyl)benzoate


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; 4.50% 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
2.244.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.86α = 90
b = 55.35β = 100.12
c = 71.49γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 6MMIRROR2020-03-06MSINGLE 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
11.7670.3898.10.000960.001040.9988.946.4214581846.872
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)
11.761.877.70.045140.050990.1490.364.222

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 REPLACEMENTTHROUGHOUT5TL81.7670.3843404230897.880.19040.18780.2391RANDOM48.165
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]
2.78-1.03-0.43-1.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.506
r_dihedral_angle_4_deg16.286
r_dihedral_angle_3_deg15.056
r_dihedral_angle_1_deg6.585
r_angle_refined_deg1.775
r_angle_other_deg1.046
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.506
r_dihedral_angle_4_deg16.286
r_dihedral_angle_3_deg15.056
r_dihedral_angle_1_deg6.585
r_angle_refined_deg1.775
r_angle_other_deg1.046
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3608
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms72

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
MOLREPphasing