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Crystal structure of the S. coelicolor AcpS in complex with acetyl- CoA at 1.5 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JBZ PDB ENTRY 2JBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M LITHIUM SULPHATE, 25% PEG 2K MME, 0.1 M SODIUM CACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.833 α = 90 b = 72.833 β = 90 c = 72.833 γ = 90
Symmetry Space Group P 21 3
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.56 50 100 0.06 32 9.4 18659 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 1.56 1.62 100 0.38 2.5 9.1
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 2JBZ 1.56 51.5 17671 956 100 0.204 0.202 0.2035 0.232 0.2328 RANDOM 21.18
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.385 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_3_deg 10.118 r_dihedral_angle_1_deg 6.263 r_scangle_it 3.872 r_scbond_it 2.854 r_mcangle_it 2.426 r_mcbond_it 1.671 r_angle_refined_deg 1.533 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.385 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_3_deg 10.118 r_dihedral_angle_1_deg 6.263 r_scangle_it 3.872 r_scbond_it 2.854 r_mcangle_it 2.426 r_mcbond_it 1.671 r_angle_refined_deg 1.533 r_nbtor_refined 0.295 r_symmetry_hbond_refined 0.261 r_xyhbond_nbd_refined 0.238 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.164 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 887 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing