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CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ACYCLOVIR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris, pH
8.0, 25%PEG 3350, and 25 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 1.79 31.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.177 α = 90 b = 135.759 β = 90 c = 41.434 γ = 90
Symmetry Space Group P 21 21 2
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 MAR scanner 300 mm plate 2009-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 33.94 90 0.08 0.08 10 7 39559 35559 2 2 20
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.2 90 0.2 0.2 3 4 2200
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1N3I 2.1 33.94 2 2 35559 31718 1679 93.92 0.18653 0.18653 0.18256 0.26197 0.254 RANDOM 23.187
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 35.267 r_dihedral_angle_4_deg 21.6 r_dihedral_angle_3_deg 18.374 r_dihedral_angle_1_deg 8.139 r_scangle_it 4.722 r_scbond_it 3.124 r_mcangle_it 2.923 r_angle_refined_deg 2.388 r_mcbond_it 1.946 r_symmetry_vdw_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 21.6 r_dihedral_angle_3_deg 18.374 r_dihedral_angle_1_deg 8.139 r_scangle_it 4.722 r_scbond_it 3.124 r_mcangle_it 2.923 r_angle_refined_deg 2.388 r_mcbond_it 1.946 r_symmetry_vdw_refined 0.341 r_nbtor_refined 0.326 r_chiral_restr 0.292 r_nbd_refined 0.267 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.19 r_bond_refined_d 0.022 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5688 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 63
Software Software Software Name Purpose MAR345dtb data collection MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement