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Structure of holo-PA1221, an NRPS protein containing adenylation and PCP domains bound to vinylsulfonamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DG8 PDB entry 4DG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 20% Methylether PEG 8000, 50 mM HEPES, 0.18 mM Val-AVS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.19 α = 90 b = 231.18 β = 90 c = 122.05 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 113 CCD MARMOSAIC 325 mm CCD SSRL 9-2 2010-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
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 2.55 55 100 0.114 9.4 3.9 25006 25006 -3 44
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 2.55 2.69 100 0.571 2.2 2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 4DG8 2.55 53.97 1.35 24977 1275 99.9 0.185 0.182 0.1739 0.237 0.2336
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] -2.0737 4.3379 -2.2642
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.071 f_angle_d 1.356 f_chiral_restr 0.095 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4314 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 50
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing PHENIX refinement MOSFLM data reduction SCALA data scaling