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Structure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other structure of a different crystal form available in the laboratory
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 273 Tris HCl pH 8.5, 0.2 M calcium chloride, PEG 4000, PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.941 α = 90 b = 70.425 β = 90 c = 148.862 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 CCD SBC-2 2000-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97933 APS 19-ID
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 2.27 60 0.064 19.8 3.9 29401 -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 2.27 2.31 95.4 0.222 5.3 3.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT structure of a different crystal form available in the laboratory 2.3 10 28994 28994 1131 95.2 0.1702 0.1702 0.196 0.23248 RANDOM 15.186
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] 3.55 -0.21 -3.35
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.189 p_scbond_it 1.851 p_mcangle_it 1.114 p_mcbond_it 0.616 p_chiral_restr 0.082 p_angle_d 0.024 p_bond_d 0.013 p_plane_restr 0.004 p_angle_deg p_planar_d
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.189 p_scbond_it 1.851 p_mcangle_it 1.114 p_mcbond_it 0.616 p_chiral_restr 0.082 p_angle_d 0.024 p_bond_d 0.013 p_plane_restr 0.004 p_angle_deg p_planar_d p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4258 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement