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Crystal structure of Lp1NTPDase from Legionella pneumophila in complex with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AAP PDB ENTRY 3AAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 20-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.701 α = 90 b = 104.701 β = 90 c = 75.415 γ = 120
Symmetry Space Group P 3 2 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 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 Australian Synchrotron MX1
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 1.65 35 97.6 0.119 14.3 7.5 55849
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) 1.65 1.74 98.8 0.452 3.5 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3AAP 1.65 20 52982 2838 96.92 0.17753 0.17645 0.1763 0.19717 0.196 RANDOM 17.487
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] 0.48 0.24 0.48 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.835 r_dihedral_angle_4_deg 20.056 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 5.097 r_scangle_it 3.865 r_scbond_it 2.886 r_mcangle_it 1.758 r_mcbond_it 1.445 r_angle_refined_deg 1.26 r_chiral_restr 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.835 r_dihedral_angle_4_deg 20.056 r_dihedral_angle_3_deg 12.365 r_dihedral_angle_1_deg 5.097 r_scangle_it 3.865 r_scbond_it 2.886 r_mcangle_it 1.758 r_mcbond_it 1.445 r_angle_refined_deg 1.26 r_chiral_restr 0.34 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2947 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 31
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling