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Crystal structure of the DYW domain of DYW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Hepes pH 7.5, 0.1 M Sodium Acetate, 0.2 M Lithium sulfate, 25%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 1.86 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.945 α = 90 b = 45.165 β = 98.04 c = 37.023 γ = 90
Symmetry Space Group P 1 21 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 2017-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.28242 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 45.17 100 0.998 12.8 6.6 10107
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.625
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 SAD THROUGHOUT 1.8 36.66 9586 507 99.98 0.18029 0.17729 0.1919 0.23365 0.2344 RANDOM 29.56
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] 0.03 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.49 r_dihedral_angle_4_deg 20.833 r_dihedral_angle_3_deg 16.65 r_long_range_B_refined 7.086 r_long_range_B_other 7.084 r_dihedral_angle_1_deg 5.856 r_scangle_other 5.451 r_scbond_it 3.623 r_scbond_other 3.62 r_mcangle_it 3.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.49 r_dihedral_angle_4_deg 20.833 r_dihedral_angle_3_deg 16.65 r_long_range_B_refined 7.086 r_long_range_B_other 7.084 r_dihedral_angle_1_deg 5.856 r_scangle_other 5.451 r_scbond_it 3.623 r_scbond_other 3.62 r_mcangle_it 3.109 r_mcangle_other 3.108 r_mcbond_it 2.124 r_mcbond_other 2.104 r_angle_refined_deg 1.524 r_angle_other_deg 1.314 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 940 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing