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Co-complex Structure of Achromobactin Synthetase Protein D (AcsD) with citrate in ATP binding site from Pectobacterium Chrysanthemi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other APO STRUCTURE OF ACSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 26%PEG8000, 0.1M TRIS-HCL PH7.8, 300MM SODIUM CITRATE ACSD WAS INCUBATED WITH 2 MM ATP-GAMMA-S (SIGMA A1388) FOR 10 MIN (RT). 3UL ACSD (6MG/ML) AND EQUAL AMOUNT OF PRECIPITANT WERE INCUBATED IN CONVENTIONAL HANGING DROP PLATES.
Crystal Properties Matthews coefficient Solvent content 2.15 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.371 α = 90 b = 94.959 β = 90 c = 160.261 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 IMAGE PLATE MARRESEARCH SINGLE SILICON (111) MONOCHROMATOR 2007-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.8 81.6 99.4 0.16 10.6 4.2 30736 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 2.8 2.95 99.9 0.41 3 4.3
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 APO STRUCTURE OF ACSD 2.8 81.65 29085 1513 98.9 0.206 0.202 0.2116 0.28 0.2847 RANDOM 11.74
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] -1.53 -1.78 3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.559 r_dihedral_angle_3_deg 18.007 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_1_deg 6.4 r_scangle_it 1.823 r_angle_refined_deg 1.461 r_scbond_it 1.096 r_mcangle_it 0.783 r_mcbond_it 0.451 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.559 r_dihedral_angle_3_deg 18.007 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_1_deg 6.4 r_scangle_it 1.823 r_angle_refined_deg 1.461 r_scbond_it 1.096 r_mcangle_it 0.783 r_mcbond_it 0.451 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.252 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.099 r_bond_refined_d 0.013 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 9215 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing