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Crystal structure of putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG condition #96 (0.2 M Lithium Sulfate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.764 α = 90 b = 42.295 β = 111.83 c = 62.287 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2013-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 50 99.3 0.07 0.07 12.9 3.7 10379 -3 55
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 2.3 2.34 92.5 0.674 2.1 3.2 480
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 3fh1 2.3 50 10348 535 98.85 0.1942 0.1926 0.2002 0.2238 0.2254 RANDOM 65.057
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] 2.65 1.2 -1.72 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.953 r_dihedral_angle_4_deg 17.038 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.046 r_mcangle_it 4.021 r_mcbond_it 2.652 r_mcbond_other 2.648 r_angle_refined_deg 1.689 r_angle_other_deg 0.992 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.953 r_dihedral_angle_4_deg 17.038 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.046 r_mcangle_it 4.021 r_mcbond_it 2.652 r_mcbond_other 2.648 r_angle_refined_deg 1.689 r_angle_other_deg 0.992 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1635 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data reduction HKL-3000 phasing HKL-3000 data scaling PHENIX phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction SCALEPACK data scaling