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Crystal structure of human JUNO (crystal form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 3% (w/v) PEG4000, 5% 2-propanol, 0.1 M HEPES-NaOH pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.77 α = 90 b = 88.579 β = 96.88 c = 108.132 γ = 90
Symmetry Space Group I 1 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 100 PIXEL DECTRIS PILATUS 2M-F 2015-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.23 44.3 99.4 8 3.4 14574
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 5JKA 3.23 44.3 13842 730 99.16 0.21773 0.21649 0.2179 0.24053 0.2381 RANDOM 72.264
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] -1.72 1.49 0.76 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.056 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 15.662 r_long_range_B_refined 8.94 r_long_range_B_other 8.94 r_dihedral_angle_1_deg 5.937 r_scangle_other 4.442 r_mcangle_it 4.007 r_mcangle_other 4.006 r_scbond_it 2.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.056 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 15.662 r_long_range_B_refined 8.94 r_long_range_B_other 8.94 r_dihedral_angle_1_deg 5.937 r_scangle_other 4.442 r_mcangle_it 4.007 r_mcangle_other 4.006 r_scbond_it 2.598 r_scbond_other 2.594 r_mcbond_it 2.351 r_mcbond_other 2.343 r_angle_refined_deg 1.443 r_angle_other_deg 1.223 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6410 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing