☰ Navigation Tabs
Crystal structure of human LC3C_8-125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.72 α = 90 b = 71.72 β = 90 c = 55.65 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2011-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.75 27.83 99.8 0.093 16.2 16985
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 1.75 1.84 100 0.366 6.3 2430
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 3VTU 1.75 27.83 16082 860 99.62 0.17358 0.17161 0.1722 0.21129 0.2134 RANDOM 23.672
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] 0.46 0.23 0.46 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.909 r_dihedral_angle_4_deg 16.606 r_dihedral_angle_3_deg 15.254 r_scangle_it 7.232 r_dihedral_angle_1_deg 6.172 r_scbond_it 4.545 r_mcangle_it 2.828 r_angle_refined_deg 2.446 r_mcbond_it 1.71 r_chiral_restr 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.909 r_dihedral_angle_4_deg 16.606 r_dihedral_angle_3_deg 15.254 r_scangle_it 7.232 r_dihedral_angle_1_deg 6.172 r_scbond_it 4.545 r_mcangle_it 2.828 r_angle_refined_deg 2.446 r_mcbond_it 1.71 r_chiral_restr 0.188 r_bond_refined_d 0.034 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 13
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling