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Dehydratase domain from CurJ module of Curacin polyketide synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 18% PEG 3350, 2-10% 1,4 butanediol, 250 mM NaCl, 100 mM bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.416 α = 90 b = 70.345 β = 90 c = 174.812 γ = 90
Symmetry Space Group P 21 21 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 2008-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97945 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 2.45 50 98.7 0.092 0.092 15.6 6.6 21789 21789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 95 0.799 0.799 2 6.3
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 3KG8 2.45 43.69 21731 20616 1115 97.71 0.19865 0.19543 0.1927 0.25849 0.2538 RANDOM 49.288
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] -2.1 2.7 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.127 r_dihedral_angle_4_deg 24.865 r_dihedral_angle_3_deg 17.552 r_dihedral_angle_1_deg 5.651 r_mcangle_it 3.585 r_scangle_it 3.41 r_scbond_it 2.505 r_mcbond_it 2.351 r_angle_refined_deg 1.171 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.127 r_dihedral_angle_4_deg 24.865 r_dihedral_angle_3_deg 17.552 r_dihedral_angle_1_deg 5.651 r_mcangle_it 3.585 r_scangle_it 3.41 r_scbond_it 2.505 r_mcbond_it 2.351 r_angle_refined_deg 1.171 r_nbtor_refined 0.308 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.084 r_bond_refined_d 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4503 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling