6Q2C

Domain-swapped dimer of Acanthamoeba castellanii CYP51


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C27 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29615% PEG 3350; 0.2 M di-sodium DL-malate, pH 6.8-7.2
Crystal Properties
Matthews coefficientSolvent content
3.0860.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.35α = 90
b = 101.57β = 90
c = 123.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 S 6Mmirrors2019-05-31MSINGLE 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)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
11.88098.20.05917.6811.41152830.344.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8583.92.860.455.4

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 REPLACEMENTFREE R-VALUE4C271.878.51109450578398.120.18740.18530.2267RANDOM49.704
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]
-0.812.42-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.937
r_dihedral_angle_4_deg16.015
r_dihedral_angle_3_deg14.948
r_long_range_B_refined8.707
r_long_range_B_other8.707
r_scangle_other7.178
r_dihedral_angle_1_deg6.276
r_mcangle_it5.348
r_mcangle_other5.347
r_scbond_it5.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.937
r_dihedral_angle_4_deg16.015
r_dihedral_angle_3_deg14.948
r_long_range_B_refined8.707
r_long_range_B_other8.707
r_scangle_other7.178
r_dihedral_angle_1_deg6.276
r_mcangle_it5.348
r_mcangle_other5.347
r_scbond_it5.095
r_scbond_other5.094
r_mcbond_it4.32
r_mcbond_other4.318
r_angle_refined_deg1.974
r_angle_other_deg1.086
r_chiral_restr0.137
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7133
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing