9GPX

The FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 12f/l


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TW7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29318% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5, 10% glycol
Crystal Properties
Matthews coefficientSolvent content
2.4549.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.193α = 90
b = 49.193β = 90
c = 196.443γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2024-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918400BESSY14.1

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
11.849.111000.0610.0660.026120.811.726718
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)
1.81.841001.4311.5570.6070.6421.812.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.835.73526645139999.9620.2250.22260.261140.03
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]
-0.224-0.112-0.2240.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.218
r_dihedral_angle_6_deg16.149
r_dihedral_angle_3_deg11.788
r_dihedral_angle_1_deg8.708
r_lrange_it6.363
r_lrange_other6.351
r_scangle_it4.595
r_scangle_other4.593
r_mcangle_it4.157
r_mcangle_other4.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.218
r_dihedral_angle_6_deg16.149
r_dihedral_angle_3_deg11.788
r_dihedral_angle_1_deg8.708
r_lrange_it6.363
r_lrange_other6.351
r_scangle_it4.595
r_scangle_other4.593
r_mcangle_it4.157
r_mcangle_other4.156
r_scbond_it3.369
r_scbond_other3.368
r_mcbond_it3.197
r_mcbond_other3.195
r_angle_refined_deg2.336
r_angle_other_deg0.788
r_symmetry_xyhbond_nbd_refined0.274
r_nbd_refined0.213
r_symmetry_nbd_other0.196
r_nbtor_refined0.185
r_symmetry_xyhbond_nbd_other0.176
r_nbd_other0.153
r_xyhbond_nbd_refined0.147
r_ncsr_local_group_10.128
r_chiral_restr0.119
r_symmetry_nbd_refined0.113
r_symmetry_nbtor_other0.093
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1874
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing