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Crystal structure of Sulfolobus acidocaldarius TrmJ in complex with S-adenosyl-L-Homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CNF PDB ENTRY 4CNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.2M KBR, 0.1 M NA-ACETATE PH 5.5, 20% PEG2000MME
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.803 α = 90 b = 54.097 β = 90 c = 130.637 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.1 43 97.5 0.06 9.5 4.1 128921 1.2
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 1.1 1.2 93.3 0.94 1.2 3.5
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 4CNF 1.1 43.26 122349 6470 97.32 0.16273 0.16156 0.1707 0.18458 0.1929 RANDOM 23.344
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] -1.02 0.72 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.414 r_sphericity_free 34.354 r_sphericity_bonded 26.08 r_rigid_bond_restr 19.329 r_dihedral_angle_4_deg 18.175 r_scbond_it 14.217 r_dihedral_angle_3_deg 13.83 r_mcangle_it 12.134 r_mcbond_other 9.895 r_mcbond_it 9.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.414 r_sphericity_free 34.354 r_sphericity_bonded 26.08 r_rigid_bond_restr 19.329 r_dihedral_angle_4_deg 18.175 r_scbond_it 14.217 r_dihedral_angle_3_deg 13.83 r_mcangle_it 12.134 r_mcbond_other 9.895 r_mcbond_it 9.89 r_dihedral_angle_1_deg 6.193 r_angle_other_deg 3.515 r_angle_refined_deg 1.547 r_chiral_restr 0.133 r_gen_planes_other 0.038 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2433 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing