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Crystal structure of E. coli MTA/SAH nucleosidase in complex with BnT-DADMeImmA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 35 % (v/v) 2-propanol, 50 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.611 α = 90 b = 69.748 β = 90 c = 127.868 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 IMAGE PLATE RIGAKU RAXIS IV 2005-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.95 63.93 96.8 0.078 24.6 15.9 34475 33372 5 5
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) 1.95 2.02 95.3 0.3 9.8 15.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1Y6Q 1.95 63.89 32720 31666 1683 96.78 0.17715 0.17715 0.17548 0.1776 0.20802 RANDOM 17.654
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] 0.52 -0.16 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.993 r_dihedral_angle_4_deg 13.772 r_dihedral_angle_3_deg 12.78 r_dihedral_angle_1_deg 5.98 r_scangle_it 2.98 r_scbond_it 1.812 r_angle_refined_deg 1.308 r_mcangle_it 1.071 r_mcbond_it 0.576 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.993 r_dihedral_angle_4_deg 13.772 r_dihedral_angle_3_deg 12.78 r_dihedral_angle_1_deg 5.98 r_scangle_it 2.98 r_scbond_it 1.812 r_angle_refined_deg 1.308 r_mcangle_it 1.071 r_mcbond_it 0.576 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3497 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling REFMAC phasing