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Crystal structure of PLP bound Diaminopropionate ammonia lyase from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.6 298 20%(w/v) PEG4000, 20%(v/v) 2-propanol, 100mM sodium citrate pH 5.6, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.89 α = 90 b = 128.44 β = 110.28 c = 138.1 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 225 mm CCD 2014-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.956 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim 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 2.5 77.16 99.9 0.13 0.15 0.07 0.98 7.5 4.6 58141 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.9 0.64 0.73 0.33 0.83 2.5 4.5
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 4D9G 2.5 77 55329 2802 99.89 0.23953 0.23651 0.234 0.29919 0.292 RANDOM 43.533
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] -0.03 -0.01 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.917 r_dihedral_angle_4_deg 18.398 r_dihedral_angle_3_deg 15.39 r_long_range_B_refined 8.035 r_long_range_B_other 8.035 r_dihedral_angle_1_deg 6.649 r_scangle_other 5.355 r_mcangle_it 5.331 r_mcangle_other 5.331 r_scbond_it 3.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.917 r_dihedral_angle_4_deg 18.398 r_dihedral_angle_3_deg 15.39 r_long_range_B_refined 8.035 r_long_range_B_other 8.035 r_dihedral_angle_1_deg 6.649 r_scangle_other 5.355 r_mcangle_it 5.331 r_mcangle_other 5.331 r_scbond_it 3.575 r_mcbond_it 3.556 r_mcbond_other 3.553 r_scbond_other 3.545 r_angle_refined_deg 1.457 r_angle_other_deg 1.107 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 10976 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement iMOSFLM data processing Aimless data scaling PHASER phasing iMOSFLM data reduction