4CRY

Direct visualisation of strain-induced protein post-translational modification


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AZDPDB ENTRY 4AZD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.420% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.4α = 90
b = 86.4β = 90
c = 81γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M2013-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.6159.197.40.0611.84.1374912
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)
11.611.6480.10.51.62.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4AZD1.6143.1935579191097.340.129720.128630.15017RANDOM26.268
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]
-3.55-3.557.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.324
r_dihedral_angle_4_deg22.95
r_dihedral_angle_3_deg15.058
r_dihedral_angle_1_deg7.099
r_scbond_it4.243
r_mcangle_it3.978
r_mcbond_it2.915
r_mcbond_other2.848
r_angle_refined_deg2.704
r_angle_other_deg1.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.324
r_dihedral_angle_4_deg22.95
r_dihedral_angle_3_deg15.058
r_dihedral_angle_1_deg7.099
r_scbond_it4.243
r_mcangle_it3.978
r_mcbond_it2.915
r_mcbond_other2.848
r_angle_refined_deg2.704
r_angle_other_deg1.121
r_chiral_restr0.174
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1997
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing