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X-ray structure of allene oxide cyclase from arabidopsis thaliana AT3G25760
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 297 10 mg/ml protein, 18.4% PEG 4K, 0.160 M POTASSIUM BROMIDE,
0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 297K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.4 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.191 α = 90 b = 66.191 β = 90 c = 212.7 γ = 120
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 HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 1.79 50 99.5 0.08 19.62 9.7 17352
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 1.79 1.83 96.7 0.31 6.212 8.6
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 1Z8K 1.79 50 16437 875 99.1 0.239 0.236 0.2376 0.283 0.2847 RANDOM 30.87
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] -0.93 -0.46 -0.93 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.594 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_4_deg 12.672 r_dihedral_angle_1_deg 6.226 r_scangle_it 5.498 r_scbond_it 4.36 r_mcangle_it 2.867 r_mcbond_it 1.748 r_angle_refined_deg 1.238 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.594 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_4_deg 12.672 r_dihedral_angle_1_deg 6.226 r_scangle_it 5.498 r_scbond_it 4.36 r_mcangle_it 2.867 r_mcbond_it 1.748 r_angle_refined_deg 1.238 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.203 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 1337 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction