4CRZ

Direct visualisation of strain-induced protein prost-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
2.5251

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.28α = 90
b = 86.28β = 90
c = 80.88γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU R-AXIS IVVARIMAX OPTICS2013-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
11.733.799.70.0413.32.4322442
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)
11.71.7499.70.42.22.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4AZD1.729.5230609163399.590.146110.144580.17519RANDOM23.383
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]
-0.32-0.320.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.68
r_dihedral_angle_4_deg18.308
r_dihedral_angle_3_deg16.015
r_dihedral_angle_1_deg6.591
r_scbond_it4.172
r_mcangle_it3.931
r_mcbond_it2.655
r_mcbond_other2.652
r_angle_refined_deg2.333
r_angle_other_deg0.977
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.68
r_dihedral_angle_4_deg18.308
r_dihedral_angle_3_deg16.015
r_dihedral_angle_1_deg6.591
r_scbond_it4.172
r_mcangle_it3.931
r_mcbond_it2.655
r_mcbond_other2.652
r_angle_refined_deg2.333
r_angle_other_deg0.977
r_chiral_restr0.144
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d0.002
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 Atoms2002
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing