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Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GAW PDB ENTRY 2GAW, polyalanine model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 PEG 4000, PEG 400, magnesium chloride, Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.296 α = 90 b = 77.624 β = 90 c = 148.152 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 MARRESEARCH Toroidal mirror 1999-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.0442 EMBL/DESY, HAMBURG X31
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 20 0.075 16.8 5.6 70249 70249 -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 1.65 1.68 89.9 0.476 2.5 5.5
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GAW, polyalanine model 1.65 19.5 69077 69077 1064 99.52 0.16349 0.16295 0.1765 0.19836 0.2095 RANDOM 10.18
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] -0.09 0.51 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 3.992 r_scangle_it 2.961 r_scbond_it 1.763 r_angle_refined_deg 1.411 r_angle_other_deg 1.105 r_mcangle_it 1.011 r_nbtor_other 0.821 r_mcbond_it 0.529 r_nbd_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 3.992 r_scangle_it 2.961 r_scbond_it 1.763 r_angle_refined_deg 1.411 r_angle_other_deg 1.105 r_mcangle_it 1.011 r_nbtor_other 0.821 r_mcbond_it 0.529 r_nbd_refined 0.3 r_symmetry_vdw_other 0.223 r_nbd_other 0.212 r_symmetry_hbond_refined 0.187 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_other 0.162 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.099 r_symmetry_hbond_other 0.08 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4240 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement