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Crystal structure of the Streptomyces coelicolor D111A AcpS mutant in complex with cofactor CoA at 1.4 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 POTASSIUM THIOCYANATE, 0.1 M SODIUM CACODYLATE PH 6.5, 8% PEG 20K PLUS 8% PEG 550 MME, 15% GLYCEROL WAS THEN ADDED AS CRYO
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.831 α = 90 b = 72.831 β = 90 c = 72.831 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 2008-02-11 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 1.4 50 99.6 0.05 34.7 7.9 25707 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 1.4 1.45 96.4 0.51 1.5 2.9
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 2JBZ 1.4 51.5 24241 1311 99.52 0.19011 0.18875 0.21498 0.2287 RANDOM 21.166
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 29.585 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 11.697 r_dihedral_angle_1_deg 5.108 r_scangle_it 3.711 r_scbond_it 2.52 r_mcangle_it 2.154 r_angle_refined_deg 1.271 r_mcbond_it 1.252 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.585 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 11.697 r_dihedral_angle_1_deg 5.108 r_scangle_it 3.711 r_scbond_it 2.52 r_mcangle_it 2.154 r_angle_refined_deg 1.271 r_mcbond_it 1.252 r_nbtor_refined 0.292 r_xyhbond_nbd_refined 0.202 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_refined 0.16 r_chiral_restr 0.068 r_bond_refined_d 0.008 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 884 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing