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Structure of aminoadipate-semialdehyde dehydrogenase- phosphopantetheinyl transferase in complex with cytosolic acyl carrier protein and coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYD PDB ENTRY 2BYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.4 M (NH4)H2PO4
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.361 α = 90 b = 69.361 β = 90 c = 184.715 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2006-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 2.7 34.7 99.9 0.09 17.9 10.4 14864
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 2.7 2.8 100 0.58 3.4 10.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BYD 2.7 50 14089 732 100 0.195 0.192 0.247 0.2826 RANDOM 50.37
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] 1.43 0.72 1.43 -2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.101 r_dihedral_angle_3_deg 19.138 r_dihedral_angle_4_deg 18.537 r_dihedral_angle_1_deg 6.799 r_scangle_it 2.114 r_angle_refined_deg 1.504 r_scbond_it 1.287 r_mcangle_it 0.896 r_angle_other_deg 0.871 r_mcbond_it 0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.101 r_dihedral_angle_3_deg 19.138 r_dihedral_angle_4_deg 18.537 r_dihedral_angle_1_deg 6.799 r_scangle_it 2.114 r_angle_refined_deg 1.504 r_scbond_it 1.287 r_mcangle_it 0.896 r_angle_other_deg 0.871 r_mcbond_it 0.506 r_symmetry_vdw_other 0.273 r_nbd_refined 0.233 r_nbd_other 0.201 r_nbtor_refined 0.2 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.105 r_nbtor_other 0.093 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2619 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing