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Crystal structure of human JUNO (crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG3350, 0.24 M malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.92 α = 90 b = 81.038 β = 90 c = 235.084 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS 2M-F 2016-02-22 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 2 50 99.2 26.6 12.3 33749
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 4KMY 2 50 32072 1674 98.97 0.19855 0.19749 0.2051 0.21782 0.2211 RANDOM 44.833
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] 3.65 -0.92 -2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.419 r_dihedral_angle_4_deg 16.724 r_dihedral_angle_3_deg 16.121 r_long_range_B_refined 6.942 r_long_range_B_other 6.941 r_dihedral_angle_1_deg 6.238 r_scangle_other 4.393 r_mcangle_it 3.535 r_mcangle_other 3.534 r_scbond_it 2.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.419 r_dihedral_angle_4_deg 16.724 r_dihedral_angle_3_deg 16.121 r_long_range_B_refined 6.942 r_long_range_B_other 6.941 r_dihedral_angle_1_deg 6.238 r_scangle_other 4.393 r_mcangle_it 3.535 r_mcangle_other 3.534 r_scbond_it 2.857 r_scbond_other 2.857 r_mcbond_it 2.366 r_mcbond_other 2.364 r_angle_refined_deg 1.476 r_angle_other_deg 1.01 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 3236 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing