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Crystal structure of the holo-acyl carrier protein (holo-AcpP) from Pseudomonas putida KT2440. Produced as an apo/holo mixture.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 0.1 M Tris Bicine buffer, pH 8.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.492 α = 90 b = 56.973 β = 90 c = 61.937 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER2 X 16M 2019-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9786 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.69 30.988 100 0.0705 0.9994 14.05 12.3 9120
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 100 0.397 9.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1T8K 1.69 30.988 9120 874 99.989 0.208 0.2047 0.2047 0.2448 0.2452 44.778
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] 0.027 0.061 -0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.664 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_3_deg 14.762 r_lrange_other 10.974 r_lrange_it 10.966 r_scangle_it 9.327 r_scangle_other 9.317 r_scbond_it 6.224 r_scbond_other 6.216 r_dihedral_angle_1_deg 6.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.664 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_3_deg 14.762 r_lrange_other 10.974 r_lrange_it 10.966 r_scangle_it 9.327 r_scangle_other 9.317 r_scbond_it 6.224 r_scbond_other 6.216 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.031 r_mcangle_other 5.029 r_mcbond_it 3.525 r_mcbond_other 3.513 r_angle_refined_deg 1.555 r_angle_other_deg 1.341 r_symmetry_xyhbond_nbd_refined 0.281 r_xyhbond_nbd_refined 0.229 r_nbd_other 0.217 r_nbd_refined 0.202 r_symmetry_nbd_other 0.183 r_symmetry_nbd_refined 0.173 r_nbtor_refined 0.154 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 651 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing