3L4D

Crystal structure of sterol 14-alpha demethylase (CYP51) from Leishmania infantum in complex with fluconazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G1Qpdb entry 3g1q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298TRIS-HCL, PEG 6000, 3,6,9,12,15-PENTAOXATRICOSAN-1-OL, FLUCONAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.891α = 90
b = 118.509β = 104.82
c = 100.96γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97850APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.745097.70.0640.06422.55.647888-387.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.742.8492.70.5580.5582.824.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3g1q2.7548.84788846715249597.550.221110.218670.2666RANDOM56.942
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]
-0.860.211.09-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.247
r_dihedral_angle_3_deg12.84
r_dihedral_angle_4_deg12.367
r_scangle_it4.968
r_dihedral_angle_1_deg3.567
r_scbond_it3.096
r_mcangle_it1.896
r_mcbond_it1.017
r_angle_refined_deg0.628
r_chiral_restr0.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.247
r_dihedral_angle_3_deg12.84
r_dihedral_angle_4_deg12.367
r_scangle_it4.968
r_dihedral_angle_1_deg3.567
r_scbond_it3.096
r_mcangle_it1.896
r_mcbond_it1.017
r_angle_refined_deg0.628
r_chiral_restr0.042
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14189
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms284

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling