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Structure of Pyrococcus horikoshii SAM hydroxide adenosyltransferase in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WU8 PDB ENTRY 1WU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 19.83% PEG 6000, 0.26M KCL, 0.1M MOPS PH 7
Crystal Properties Matthews coefficient Solvent content 1 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.561 α = 90 b = 65.561 β = 90 c = 142.685 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 ADSC CCD TORODIAL FOCUSING MIRROR 2008-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.77 50 99.7 0.04 11.4 4.6 22346 2
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 1.77 1.83 100 0.5 3.6 3.7
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 PDB ENTRY 1WU8 1.77 52.78 21127 1137 99.66 0.17039 0.16796 0.1727 0.21739 0.2154 RANDOM 33.439
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] -1.57 -0.78 -1.57 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_3_deg 13.528 r_dihedral_angle_1_deg 6.654 r_scangle_it 3.117 r_scbond_it 2.331 r_angle_refined_deg 1.623 r_mcangle_it 1.301 r_mcbond_it 1.146 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_3_deg 13.528 r_dihedral_angle_1_deg 6.654 r_scangle_it 3.117 r_scbond_it 2.331 r_angle_refined_deg 1.623 r_mcangle_it 1.301 r_mcbond_it 1.146 r_angle_other_deg 0.959 r_symmetry_vdw_other 0.266 r_mcbond_other 0.261 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.212 r_nbd_other 0.211 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.109 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2031 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing