7GAH

PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z2033637875


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.729336% PEG 8000, 0.1M acetate pH 4.7
Crystal Properties
Matthews coefficientSolvent content
2.2344.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.2α = 90
b = 61.2β = 90
c = 35.27γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-02-09SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92124DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.930.61000.1270.1330.0380.9971513.210488
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.951002.8782.9850.7870.36514.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT8Q531.930.581005342199.870.20080.19860.2541RANDOM47.276
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]
-0.54-0.541.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.882
r_dihedral_angle_4_deg20.499
r_dihedral_angle_3_deg14.916
r_dihedral_angle_1_deg6.119
r_mcangle_it4.922
r_mcbond_it3.469
r_mcbond_other3.465
r_angle_refined_deg1.628
r_angle_other_deg1.239
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.882
r_dihedral_angle_4_deg20.499
r_dihedral_angle_3_deg14.916
r_dihedral_angle_1_deg6.119
r_mcangle_it4.922
r_mcbond_it3.469
r_mcbond_other3.465
r_angle_refined_deg1.628
r_angle_other_deg1.239
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms954
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing