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Crystal structure of potassium-independent plant asparaginase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K2X PDB ENTRY 1K2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 20% PEG 4000, 100 mM HEPES, 200 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.68 α = 100.6 b = 60.2 β = 92.9 c = 114.63 γ = 113.4
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 MARRESEARCH 2004-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 EMBL/DESY, HAMBURG X11
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 2.6 25 99 0.073 14.3 2.8 34621 34621 -3 40.9
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 2.6 2.69 96.9 0.152 6.1 2.5 3371
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 (All) 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 PDB ENTRY 1K2X 2.6 25 34621 32880 1741 98.9 0.192 0.192 0.189 0.203 0.254 RANDOM 25.11
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] -1.13 1.3 0.02 4.16 0.19 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.956 r_scangle_it 2.538 r_angle_refined_deg 1.584 r_scbond_it 1.479 r_mcangle_it 0.879 r_mcbond_it 0.477 r_nbd_refined 0.225 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.956 r_scangle_it 2.538 r_angle_refined_deg 1.584 r_scbond_it 1.479 r_mcangle_it 0.879 r_mcbond_it 0.477 r_nbd_refined 0.225 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.085 r_metal_ion_refined 0.066 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8693 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing