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Room temperature crystal structure of Helicobacter pylori L- asparaginase at 1.8 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 17.5% (W/V) PEG 4000, 0.1 M MG FORMATE, 0.1 M HEPES-NAOH, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.909 α = 90 b = 96.369 β = 90 c = 101.868 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD MARRESEARCH BENT VERTICAL FOCUSSING 2009-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 99 99.9 0.07 24.8 11.1 29828 -3
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 1.83 99 0.5 3.5 11.4
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 OTHER THROUGHOUT NONE 1.8 70.01 28339 1474 99.93 0.15321 0.1516 0.155 0.18477 0.1896 RANDOM 14.939
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 0.08 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.54 r_dihedral_angle_4_deg 16.619 r_dihedral_angle_3_deg 12.528 r_dihedral_angle_1_deg 5.455 r_scangle_it 3.451 r_scbond_it 2.247 r_mcangle_it 1.343 r_angle_refined_deg 1.321 r_mcbond_it 0.846 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.54 r_dihedral_angle_4_deg 16.619 r_dihedral_angle_3_deg 12.528 r_dihedral_angle_1_deg 5.455 r_scangle_it 3.451 r_scbond_it 2.247 r_mcangle_it 1.343 r_angle_refined_deg 1.321 r_mcbond_it 0.846 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.284 r_symmetry_hbond_refined 0.261 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 2373 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling