X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP323PEG400, Potassium chloride, Calcium chloride, Sodium cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.42α = 90
b = 120.743β = 102.05
c = 184.653γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9762ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8100.37900.0540.0470.9988.81.9252686
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8391.10.520.4550.6431.61.8

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 REPLACEMENTTHROUGHOUT4AUM1.890.462119101126889.860.159610.157840.19297RANDOM26.712
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]
-1.19-0.840.790.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.908
r_dihedral_angle_4_deg17.281
r_dihedral_angle_3_deg12.678
r_dihedral_angle_1_deg7.096
r_long_range_B_refined4.594
r_long_range_B_other4.594
r_scangle_other2.603
r_mcangle_it1.92
r_mcangle_other1.92
r_angle_refined_deg1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.908
r_dihedral_angle_4_deg17.281
r_dihedral_angle_3_deg12.678
r_dihedral_angle_1_deg7.096
r_long_range_B_refined4.594
r_long_range_B_other4.594
r_scangle_other2.603
r_mcangle_it1.92
r_mcangle_other1.92
r_angle_refined_deg1.78
r_scbond_it1.713
r_scbond_other1.713
r_mcbond_it1.332
r_mcbond_other1.331
r_angle_other_deg1.042
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21153
Nucleic Acid Atoms
Solvent Atoms2030
Heterogen Atoms193

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling