7GAP

PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z728939702


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
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.215α = 90
b = 61.215β = 90
c = 35.379γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-02-10SINGLE 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
11.6830.6399.60.1530.1590.0430.9779.913.715116
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)
11.681.7198.85.5525.7611.530.32714

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 SYNTHESISTHROUGHOUT8Q531.6830.651435867499.030.20450.20280.2436RANDOM35.028
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]
-0.48-0.480.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.18
r_dihedral_angle_4_deg23.692
r_dihedral_angle_3_deg13.83
r_dihedral_angle_1_deg6.02
r_mcangle_it3.706
r_mcbond_other2.548
r_mcbond_it2.546
r_angle_refined_deg1.494
r_angle_other_deg1.261
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.18
r_dihedral_angle_4_deg23.692
r_dihedral_angle_3_deg13.83
r_dihedral_angle_1_deg6.02
r_mcangle_it3.706
r_mcbond_other2.548
r_mcbond_it2.546
r_angle_refined_deg1.494
r_angle_other_deg1.261
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms954
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing