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)
Type	Source	Accession Code	Details
experimental model	PDB	5TL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	296	30 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 coefficient	Solvent content
2.22	44.69

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	PIXEL	DECTRIS PILATUS3 6M	MIRRORS	2021-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.81	70.94	93.7	0.00056	0.00062	0.999	12.19	6.069		40431			55.33

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)	Redundancy	Number Unique Reflections (All)
1	1.81	1.86	58.7		0.0355	0.04134	0.123	0.36	3.57

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5TL8	1.81	70.94	38337	2020	93.46	0.1915	0.189	0.24	RANDOM	60.927

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	-2.37		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.749
r_dihedral_angle_4_deg	17.693
r_dihedral_angle_3_deg	16.832
r_dihedral_angle_1_deg	6.636
r_angle_refined_deg	1.864
r_angle_other_deg	1.594
r_chiral_restr	0.116
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.749
r_dihedral_angle_4_deg	17.693
r_dihedral_angle_3_deg	16.832
r_dihedral_angle_1_deg	6.636
r_angle_refined_deg	1.864
r_angle_other_deg	1.594
r_chiral_restr	0.116
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3600
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.