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OYE2 from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 0.1 M sodium citrate, pH 5, 16% (v/v) PEG 10 000
Crystal Properties Matthews coefficient Solvent content 2.25 45.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.745 α = 90 b = 101.265 β = 90 c = 160.856 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 93 PIXEL DECTRIS PILATUS 6M 2018-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.529 47.228 99.8 0.12 0.136 0.063 0.997 9.9 4.6 122425
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.529 1.555 100 1.255 1.429 0.673 0.35 1.8 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.529 47.228 116355 6069 99.83 0.17799 0.17672 0.1884 0.20249 0.2102 RANDOM 16.989
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 19.03 r_dihedral_angle_3_deg 13.29 r_dihedral_angle_1_deg 6.636 r_long_range_B_refined 4.929 r_long_range_B_other 4.879 r_scangle_other 4.169 r_scbond_other 2.686 r_scbond_it 2.685 r_mcangle_it 2.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 19.03 r_dihedral_angle_3_deg 13.29 r_dihedral_angle_1_deg 6.636 r_long_range_B_refined 4.929 r_long_range_B_other 4.879 r_scangle_other 4.169 r_scbond_other 2.686 r_scbond_it 2.685 r_mcangle_it 2.144 r_mcangle_other 2.144 r_angle_refined_deg 1.707 r_angle_other_deg 1.522 r_mcbond_it 1.464 r_mcbond_other 1.456 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 6247 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement Aimless data scaling autoPROC data processing XDS data reduction PHASER phasing