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Co-complex Structure of Achromobactin Synthetase Protein D (AcsD) with ATP 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 7.8 298 0.1 M TRIS-HCL PH 7.8, 26% (W/V) PEG8000, 300 MM L-SERINE. 5MM ATP (DISSOLVED IN WATER) WAS PRE-INCUBATED FOR 10 MIN (RT) WITH 6 MG/ML ACSD. PROTEINULLTP PRECIPITATE WAS REMOVED BY CENTRIFUGATION. 1 UL OF SUPERNATANT AND EQUAL AMOUNT OF PRECIPITANT WAS USED IN HANGING DROP CRYSTALLIZATION (298 K).
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.874 α = 90 b = 94.542 β = 90 c = 157.77 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 CCD ADSC CCD TOROIDAL ZERODUR MIRROR 2007-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.2 81.1 99.9 0.11 15.7 10.1 61355 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 2.95 99.9 0.38 5.9 7.3
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 2.2 81.11 58259 3096 99.9 0.219 0.216 0.2291 0.277 0.2929 RANDOM 12.34
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] -2.69 -3.08 5.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.95 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 15.318 r_dihedral_angle_1_deg 6.18 r_scangle_it 1.939 r_angle_refined_deg 1.333 r_scbond_it 1.278 r_mcangle_it 0.823 r_mcbond_it 0.495 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.95 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 15.318 r_dihedral_angle_1_deg 6.18 r_scangle_it 1.939 r_angle_refined_deg 1.333 r_scbond_it 1.278 r_mcangle_it 0.823 r_mcbond_it 0.495 r_nbtor_refined 0.309 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.086 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 9252 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALA data scaling PHASER phasing