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Crystal structure of a C-terminally truncated CYT-18 protein including N-terminal residues
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y42
Crystallization Crystal Properties Matthews coefficient Solvent content 2.26 45.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.88 α = 90 b = 73.21 β = 111.35 c = 56.79 γ = 90
Symmetry Space Group C 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.54
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 1.95 58.58 94.87 25832 25832
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 1Y42 1.95 58.58 25832 1936 94.87 0.17081 0.16727 0.185 0.21125 0.2236 RANDOM 32.789
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] 0.2 0.43 -1.53 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.08 r_dihedral_angle_4_deg 13.673 r_dihedral_angle_3_deg 12.532 r_long_range_B_refined 7.094 r_long_range_B_other 7.029 r_dihedral_angle_1_deg 5.455 r_scangle_other 4.263 r_mcangle_other 3.545 r_mcangle_it 3.54 r_scbond_it 2.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.08 r_dihedral_angle_4_deg 13.673 r_dihedral_angle_3_deg 12.532 r_long_range_B_refined 7.094 r_long_range_B_other 7.029 r_dihedral_angle_1_deg 5.455 r_scangle_other 4.263 r_mcangle_other 3.545 r_mcangle_it 3.54 r_scbond_it 2.695 r_scbond_other 2.694 r_mcbond_it 2.33 r_mcbond_other 2.321 r_angle_refined_deg 1.127 r_angle_other_deg 0.736 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3071 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement