7RTQ

Sterol 14alpha demethylase (CYP51) from Naegleria fowleri in complex with an inhibitor R)-N-(1-(3,4'-difluorobiphenyl-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G1Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.34 mM n-Dodecyl-beta-D-maltoside, 5.54 mM TCEP, 15% PEG 3350 (w/v), 5% isopropanol , 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.3447

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.062α = 89.49
b = 75.223β = 74.63
c = 105.953γ = 63.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe lens2021-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.1167.0896.80.0730.0990.0730.9958.63.311399623.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.2970.4140.6130.3390.7782.43.3

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 REPLACEMENTTHROUGHOUT3g1q2.1164.63105350572596.810.21270.21130.2373RANDOM28.549
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]
-0.14-0.030.080.10.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.051
r_dihedral_angle_4_deg18.154
r_dihedral_angle_3_deg15.707
r_dihedral_angle_1_deg7.163
r_rigid_bond_restr3.916
r_angle_other_deg1.52
r_angle_refined_deg1.449
r_chiral_restr0.07
r_gen_planes_other0.02
r_bond_other_d0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.051
r_dihedral_angle_4_deg18.154
r_dihedral_angle_3_deg15.707
r_dihedral_angle_1_deg7.163
r_rigid_bond_restr3.916
r_angle_other_deg1.52
r_angle_refined_deg1.449
r_chiral_restr0.07
r_gen_planes_other0.02
r_bond_other_d0.017
r_gen_planes_refined0.014
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14468
Nucleic Acid Atoms
Solvent Atoms941
Heterogen Atoms508

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing