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apo-structure of YTH domain of SpMmi1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG3350, 0.1M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2 38.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.836 α = 90 b = 60.261 β = 90 c = 119.614 γ = 90
Symmetry Space Group P 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 CCD RIGAKU 2014-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
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 1.49 59.81 98.5 16.96 11.8 40097
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 THROUGHOUT 1.49 59.81 38091 2006 98.49 0.1954 0.19356 0.2033 0.2298 0.243 RANDOM 18.951
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] 0.83 -0.17 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.894 r_dihedral_angle_3_deg 11.936 r_dihedral_angle_4_deg 11.84 r_dihedral_angle_1_deg 6.599 r_long_range_B_refined 5.895 r_long_range_B_other 5.895 r_scangle_other 4.203 r_scbond_it 2.792 r_scbond_other 2.791 r_mcangle_it 2.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.894 r_dihedral_angle_3_deg 11.936 r_dihedral_angle_4_deg 11.84 r_dihedral_angle_1_deg 6.599 r_long_range_B_refined 5.895 r_long_range_B_other 5.895 r_scangle_other 4.203 r_scbond_it 2.792 r_scbond_other 2.791 r_mcangle_it 2.594 r_mcangle_other 2.593 r_angle_refined_deg 2.003 r_mcbond_it 1.794 r_mcbond_other 1.756 r_angle_other_deg 1.094 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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 2130 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot data reduction HKL-2000 data scaling PHASER phasing