7RKR | pdb_00007rkr

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)
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; 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 coefficient	Solvent content
2.2	44.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.86	α = 90
b = 55.35	β = 100.12
c = 71.49	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	MIRROR	2020-03-06	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	1.76	70.38	98.1	0.00096	0.00104	0.998	8.94	6.421		45818			46.872

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)	Redundancy	Number Unique Reflections (All)
1	1.76	1.8	77.7		0.04514	0.05099	0.149	0.36	4.222

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5TL8	1.76	70.38	43404	2308	97.88	0.1904	0.1878	0.2	0.2391	0.24	RANDOM	48.165

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.506
r_dihedral_angle_4_deg	16.286
r_dihedral_angle_3_deg	15.056
r_dihedral_angle_1_deg	6.585
r_angle_refined_deg	1.775
r_angle_other_deg	1.046
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.506
r_dihedral_angle_4_deg	16.286
r_dihedral_angle_3_deg	15.056
r_dihedral_angle_1_deg	6.585
r_angle_refined_deg	1.775
r_angle_other_deg	1.046
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3608
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	72

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
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.