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Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 PEG2000, HEPES 7.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.097 α = 90 b = 71.202 β = 118 c = 142.6 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 300 mm CCD 2015-10-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 30 97.5 0.04 0.999 17.99 3.14 166478 -3 25.71
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 1.6 1.7 98.2 0.383 3.17 26952
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WSA 1.6 30 155768 8241 96.16 0.1676 0.1659 0.2013 0.1741 RANDOM 23.727
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] 0.06 0.31 -0.12 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.038 r_dihedral_angle_4_deg 19.947 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 6.477 r_mcangle_it 3.039 r_mcbond_it 2.21 r_mcbond_other 2.208 r_angle_refined_deg 1.895 r_angle_other_deg 1.508 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.038 r_dihedral_angle_4_deg 19.947 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 6.477 r_mcangle_it 3.039 r_mcbond_it 2.21 r_mcbond_other 2.208 r_angle_refined_deg 1.895 r_angle_other_deg 1.508 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9732 Nucleic Acid Atoms Solvent Atoms 1367 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing XDS data scaling