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Crystal structure of Escherichia coli Diaminopropionate ammonia lyase in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D9I PDB ENTRY 4D9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 298 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 5mM beta mercaptoethanol, 40mM tris HCl pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.778 α = 90 b = 94.145 β = 110.01 c = 94.687 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU JUPITER 210 bending magnet 2006-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 2.19 50 98.3 0.078 18.9 3.6 71324 36.3
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 2.2 2.28 97.5 0.357 2.48 3.4 7006
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 PDB ENTRY 4D9I 2.19 40.65 67710 3590 98.03 0.21574 0.21338 0.2124 0.26065 0.2598 RANDOM 42.953
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 -0.04 -0.01 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_3_deg 13.879 r_dihedral_angle_4_deg 10.318 r_dihedral_angle_1_deg 4.853 r_angle_refined_deg 1.022 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_3_deg 13.879 r_dihedral_angle_4_deg 10.318 r_dihedral_angle_1_deg 4.853 r_angle_refined_deg 1.022 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 11015 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling