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Crystal structure of human LC3B_2-119
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ECI PDB ENTRY 3ECI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 2.0M Ammonium sulfate, 0.1M Tri-sodium citrate, 0.2M Potassium sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.68 α = 90 b = 53.55 β = 90 c = 61.02 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2010-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 22.91 99 0.063 22.1 15380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 98.5 0.373 5.5 2184
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ECI 1.6 22.91 14550 775 98.43 0.1835 0.18109 0.1792 0.23121 0.2281 RANDOM 17.097
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] 0.67 -0.45 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.304 r_dihedral_angle_4_deg 23.393 r_dihedral_angle_3_deg 12.6 r_scangle_it 6.238 r_dihedral_angle_1_deg 6.193 r_scbond_it 4.055 r_mcangle_it 2.701 r_angle_refined_deg 2.364 r_mcbond_it 1.596 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.304 r_dihedral_angle_4_deg 23.393 r_dihedral_angle_3_deg 12.6 r_scangle_it 6.238 r_dihedral_angle_1_deg 6.193 r_scbond_it 4.055 r_mcangle_it 2.701 r_angle_refined_deg 2.364 r_mcbond_it 1.596 r_chiral_restr 0.178 r_bond_refined_d 0.027 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1015 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 25
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling