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Structural basis for allene oxide cyclization in moss
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 292 Hampton Magic Screen condition no. 49 containing 20 % (w/v) PEG 8000, 0.1 M Na3PO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.42 α = 84.36 b = 67.513 β = 79.15 c = 161.879 γ = 62.13
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 225 mm CCD MIRRORS 2008-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.35 19.85 92.8 0.031 15.1 2.2 505495 -3 23.15
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 1.35 1.45 84.2 0.478 2.1
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 2DIO 1.35 19.85 505495 480301 25280 92.8 0.143 0.141 0.1433 0.169 0.1713 THIN SHELLS (NCS) 29.47
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] -1.29 0.95 0.48 -0.11 -0.34 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.432 r_sphericity_free 28.897 r_sphericity_bonded 19.957 r_dihedral_angle_4_deg 15.679 r_dihedral_angle_3_deg 11.546 r_rigid_bond_restr 9.371 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.42 r_chiral_restr 0.079 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.432 r_sphericity_free 28.897 r_sphericity_bonded 19.957 r_dihedral_angle_4_deg 15.679 r_dihedral_angle_3_deg 11.546 r_rigid_bond_restr 9.371 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.42 r_chiral_restr 0.079 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16824 Nucleic Acid Atoms Solvent Atoms 2571 Heterogen Atoms 300
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing