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Mn2+ and Zn2+ requirements for the lariat debranching enzyme, Dbr1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 24% PEG 8000, 0.1 M HEPES, pH 7.5, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.22 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.341 α = 90 b = 70.92 β = 90 c = 109.266 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 95 CCD ADSC QUANTUM 315 2012-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1, 1.28, 1.30 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 50 100 0.074 34.1 12.1 35775
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 0.529 3.81 12.2
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 41.88 30215 1616 95.29 0.17393 0.17197 0.1813 0.21027 0.2171 RANDOM 31.416
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] -0.02 0.11 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.553 r_dihedral_angle_4_deg 17.98 r_dihedral_angle_3_deg 13.94 r_dihedral_angle_1_deg 6.413 r_angle_refined_deg 1.788 r_angle_other_deg 0.881 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.553 r_dihedral_angle_4_deg 17.98 r_dihedral_angle_3_deg 13.94 r_dihedral_angle_1_deg 6.413 r_angle_refined_deg 1.788 r_angle_other_deg 0.881 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2861 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHELXCD phasing