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Dehydratase domain from CurF module of Curacin polyketide synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 293 14% (w/v) PEG 4000, 200 mM CaCl2, 10% (v/v) glycerol, 2 mM DTT, 100 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.379 α = 90 b = 198.385 β = 90 c = 146.764 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 CCD MARMOSAIC 300 mm CCD MIRRORS 2007-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 2.7 50 100 0.109 0.109 18.1 7.4 35542
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 2.7 2.8 100 0.792 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3KG7 2.7 41.89 35270 33290 1980 99.16 0.21549 0.21254 0.2081 0.2651 0.2604 RANDOM 70.591
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] -3.06 -1.42 4.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.279 r_dihedral_angle_3_deg 15.946 r_dihedral_angle_4_deg 13.981 r_dihedral_angle_1_deg 5.025 r_mcangle_it 1.389 r_angle_refined_deg 0.918 r_scangle_it 0.885 r_mcbond_it 0.809 r_scbond_it 0.58 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.279 r_dihedral_angle_3_deg 15.946 r_dihedral_angle_4_deg 13.981 r_dihedral_angle_1_deg 5.025 r_mcangle_it 1.389 r_angle_refined_deg 0.918 r_scangle_it 0.885 r_mcbond_it 0.809 r_scbond_it 0.58 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.185 r_nbd_refined 0.172 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.061 r_symmetry_metal_ion_refined 0.056 r_metal_ion_refined 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8802 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling