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Crystal structure of Indole-3-acetic Acid Methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6E CLARKIA BREWERI CBSAMT (PDB CODE: 1M6E)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 PEG 20,000, 1 M urea, 0.3 M KNO3, 100 mM MOPSO-Na+ and 3 mM SAH, EVAPORATION, temperature 277K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 3.36 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.27 α = 90 b = 129.4 β = 112.3 c = 68.33 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 210 DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING 2003-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 2.75 50 72.4 0.116 0.094 12.14 2.97 21631
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 2.75 2.82 79.5 0.478 0.469 2.72 2.93
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 CLARKIA BREWERI CBSAMT (PDB CODE: 1M6E) 2.75 45.22 28223 20940 1090 74.4 0.258 0.257 0.2517 0.282 0.2785 RANDOM 50.85
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] 1.21 -1.3 -1.21 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.344 r_dihedral_angle_3_deg 22.426 r_dihedral_angle_4_deg 19.748 r_dihedral_angle_1_deg 5.229 r_scangle_it 2.334 r_mcangle_it 1.847 r_angle_refined_deg 1.448 r_scbond_it 1.408 r_mcbond_it 1.02 r_symmetry_vdw_refined 0.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.344 r_dihedral_angle_3_deg 22.426 r_dihedral_angle_4_deg 19.748 r_dihedral_angle_1_deg 5.229 r_scangle_it 2.334 r_mcangle_it 1.847 r_angle_refined_deg 1.448 r_scbond_it 1.408 r_mcbond_it 1.02 r_symmetry_vdw_refined 0.387 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.096 r_bond_refined_d 0.012 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 5278 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 54
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction