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L-asparaginase from Erwinia carotovora in complex with aspartic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZCF pdb entry 1ZCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 12% MMEPEG 5000, 0.03% b-D-glucopiranoside, 0.02% sodium azide, 20 mm aspartic acid sodium salt, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.061 α = 90 b = 135.88 β = 90 c = 251.525 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 MAR CCD 165 mm bent mirror 2005-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.98 EMBL/DESY, HAMBURG BW7A
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 1.9 20 97.2 0.048 31.3 3.7 191790 191790
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 1.9 1.92 88.1 0.224 5.5 3.2 5744
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1ZCF 1.9 14.99 181808 181808 9647 97.25 0.219 0.206 0.204 0.2024 0.229 0.2271 RANDOM 27.126
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] 0.21 0.01 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.566 r_scangle_it 11.733 r_scbond_it 8.793 r_dihedral_angle_3_deg 8.356 r_dihedral_angle_4_deg 8.299 r_mcangle_it 6.164 r_mcbond_it 5.571 r_dihedral_angle_1_deg 2.689 r_angle_refined_deg 0.941 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.566 r_scangle_it 11.733 r_scbond_it 8.793 r_dihedral_angle_3_deg 8.356 r_dihedral_angle_4_deg 8.299 r_mcangle_it 6.164 r_mcbond_it 5.571 r_dihedral_angle_1_deg 2.689 r_angle_refined_deg 0.941 r_nbtor_refined 0.302 r_nbd_refined 0.142 r_symmetry_hbond_refined 0.116 r_xyhbond_nbd_refined 0.11 r_symmetry_vdw_refined 0.091 r_chiral_restr 0.088 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19296 Nucleic Acid Atoms Solvent Atoms 2301 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing