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
2.2745.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.33α = 90
b = 99.982β = 97.66
c = 110.422γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97ESRFID30B

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
11.930970.06310.92.7130980
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)
11.920.4442.3

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 REPLACEMENTTHROUGHOUT4LC31.9301309806467970.2380.2360.265RANDOM28.3
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]
-0.090.04-0.060.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.034
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg13.769
r_dihedral_angle_1_deg6.335
r_long_range_B_refined3.887
r_long_range_B_other3.794
r_angle_refined_deg1.572
r_angle_other_deg1.371
r_scangle_other1.146
r_mcangle_it1.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.034
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg13.769
r_dihedral_angle_1_deg6.335
r_long_range_B_refined3.887
r_long_range_B_other3.794
r_angle_refined_deg1.572
r_angle_other_deg1.371
r_scangle_other1.146
r_mcangle_it1.081
r_mcangle_other1.081
r_scbond_it0.7
r_scbond_other0.7
r_mcbond_it0.646
r_mcbond_other0.646
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.008
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 Atoms12564
Nucleic Acid Atoms
Solvent Atoms713
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing