3WAL | pdb_00003wal

Crystal structure of human LC3A_2-121


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VTU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52930.2M Sodium malonate, 20% PEG 3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.98α = 90
b = 92.98β = 90
c = 33.09γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2010-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98000Photon FactoryBL-17A

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
1246.51000.07418.29793
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)
122.111000.3825.11422

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3VTU232.89931347099.890.18420.181470.190.236930.24RANDOM35.092
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]
-0.74-0.741.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.456
r_dihedral_angle_4_deg19.298
r_dihedral_angle_3_deg16.329
r_dihedral_angle_1_deg6.752
r_angle_refined_deg1.943
r_angle_other_deg0.918
r_chiral_restr0.107
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.456
r_dihedral_angle_4_deg19.298
r_dihedral_angle_3_deg16.329
r_dihedral_angle_1_deg6.752
r_angle_refined_deg1.943
r_angle_other_deg0.918
r_chiral_restr0.107
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms960
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms9

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling