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CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH ATP AND N-CITRYL-ETHYLENEDIAMINE FROM PECTOBACTERIUM CHRYSANTHEMI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FFE PDB ENTRY 3FFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 FOR CO-CRYSTALLIZATION WITH N-CITRYL-ETHYLENEDIAMINE 9 MG/ML WT ACSD (STORED IN PROTEIN BUFFER: 50 MM TRIS-HCL PH 7.5, 500 MM NACL, 10 % GLYCEROL) WAS INCUBATED FOR ONE HOUR WITH 15 MM ETHYLENEDIAMINE, 10 MM MGCL2, 15 MM ATP AND 15 MM CITRATE. THE SUPERNATANT WAS USED TO GROW N-CITRYL-ETHYLENEDIAMINE CO-COMPLEX CRYSTALS IN HANGING DROPS FROM EQUAL MIXTURES WITH 0.1 M HEPES PH 7.2, 17% PEG 8000, 7.5% (V/V) GLYCEROL AT 20C
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.704 α = 97.26 b = 71.521 β = 101.97 c = 95.595 γ = 91.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2008-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 50 93.8 0.06 12.8 3.1 89038 2
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 2.07 74.7 0.35 2.7 2.7
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 3FFE 2 92.85 89038 4680 93.59 0.19204 0.18994 0.1922 0.23129 0.2331 RANDOM 38.189
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] -0.72 -3.34 -1.85 2.66 0.92 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.732 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_1_deg 5.781 r_scangle_it 2.705 r_scbond_it 1.733 r_angle_refined_deg 1.264 r_mcangle_it 1.256 r_mcbond_it 0.75 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.732 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_1_deg 5.781 r_scangle_it 2.705 r_scbond_it 1.733 r_angle_refined_deg 1.264 r_mcangle_it 1.256 r_mcbond_it 0.75 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9323 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing