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CurF ER cyclopropanase from curacin A biosynthetic pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M HEPES pH 7.5, 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.906 α = 90 b = 47.294 β = 123.44 c = 76.902 γ = 90
Symmetry Space Group C 1 2 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 2012-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.72932 APS 23-ID-D
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 0.96 30 99.4 0.08 9.5 3.7 197326
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 5DOZ 0.96 30 187338 9948 99.32 0.11724 0.11652 0.1163 0.13058 0.1303 RANDOM 11.994
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] 0.06 -0.14 0.09 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.472 r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 16.731 r_sphericity_bonded 12.123 r_dihedral_angle_3_deg 11.424 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 5.637 r_long_range_B_other 5.636 r_rigid_bond_restr 2.425 r_scangle_other 2.301
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.472 r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 16.731 r_sphericity_bonded 12.123 r_dihedral_angle_3_deg 11.424 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 5.637 r_long_range_B_other 5.636 r_rigid_bond_restr 2.425 r_scangle_other 2.301 r_scbond_it 1.902 r_scbond_other 1.902 r_angle_refined_deg 1.513 r_mcangle_it 1.265 r_mcangle_other 1.265 r_mcbond_it 0.939 r_mcbond_other 0.937 r_angle_other_deg 0.814 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2647 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing