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Structure determination and refinement at 2.44 A resolution of Argininosuccinate lyase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K7W PDB entry 1K7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 Ammonium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.14 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.469 α = 90 b = 121.469 β = 90 c = 255.251 γ = 120
Symmetry Space Group P 61 2 2
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 Bent mirror 2002-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.134 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.44 35 99.8 0.099 0.074 20.7 14.37 42164 35.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.53 98.7 0.401 0.437 6.06 4091
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1K7W 2.44 20 39912 39912 2021 99.81 0.1694 0.16942 0.16689 0.21742 0.2561 RANDOM 19.764
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.603 r_scangle_it 3.515 r_scbond_it 2.17 r_angle_refined_deg 1.537 r_mcangle_it 1.093 r_mcbond_it 0.546 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.603 r_scangle_it 3.515 r_scbond_it 2.17 r_angle_refined_deg 1.537 r_mcangle_it 1.093 r_mcbond_it 0.546 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7012 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling CNS phasing