X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LC3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.150.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8 000
Crystal Properties
Matthews coefficientSolvent content
2.1943.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.008α = 90
b = 99.324β = 97.74
c = 107.608γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.97BESSY14.1

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
12.229.7950.0986.42.179389
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)
12.22.30.5012

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 REPLACEMENTTHROUGHOUT4LC32.229.7793893866950.2410.2380.288RANDOM24.2
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]
-1.360.19-1.953.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.432
r_dihedral_angle_4_deg15.953
r_dihedral_angle_3_deg13.968
r_dihedral_angle_1_deg6.689
r_long_range_B_refined5.212
r_long_range_B_other5.112
r_scangle_other3.165
r_mcangle_it2.887
r_mcangle_other2.887
r_scbond_it2.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.432
r_dihedral_angle_4_deg15.953
r_dihedral_angle_3_deg13.968
r_dihedral_angle_1_deg6.689
r_long_range_B_refined5.212
r_long_range_B_other5.112
r_scangle_other3.165
r_mcangle_it2.887
r_mcangle_other2.887
r_scbond_it2.014
r_scbond_other2.014
r_mcbond_it1.829
r_mcbond_other1.828
r_angle_refined_deg1.614
r_angle_other_deg1.203
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms12506
Nucleic Acid Atoms
Solvent Atoms817
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing