☰ Navigation Tabs
The thermostable L-asparaginase from Thermococcus kodakarensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 294 0.09 M NPS, 0.1 M buffer system 2, pH 6.5-7.0, 28.5% (v/v) EDO_P8K from the Morpheus kit
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.74 α = 72.13 b = 70.96 β = 76.22 c = 107.73 γ = 87.83
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2016-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.18 99.58 97.4 0.06 0.07 1 10.06 3.5 98478 50
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.26 97.2 1.2 1.4 0.75 0.59 1.3 3.6
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 1WLS 2.18 68.65 93578 4896 97.5 0.19536 0.19379 0.1981 0.22391 0.2279 RANDOM 77.078
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] -0.46 1.33 1.14 0.01 -0.57 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.071 r_dihedral_angle_4_deg 19.013 r_dihedral_angle_3_deg 16.715 r_dihedral_angle_1_deg 7.279 r_long_range_B_refined 6.747 r_long_range_B_other 6.747 r_scangle_other 4.342 r_mcangle_it 3.885 r_mcangle_other 3.885 r_scbond_it 2.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.071 r_dihedral_angle_4_deg 19.013 r_dihedral_angle_3_deg 16.715 r_dihedral_angle_1_deg 7.279 r_long_range_B_refined 6.747 r_long_range_B_other 6.747 r_scangle_other 4.342 r_mcangle_it 3.885 r_mcangle_other 3.885 r_scbond_it 2.773 r_scbond_other 2.773 r_mcbond_it 2.447 r_mcbond_other 2.446 r_angle_refined_deg 2.105 r_angle_other_deg 1.14 r_chiral_restr 0.138 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15042 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PHASER phasing Coot model building xia2 data reduction Aimless data scaling