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Crystal structure of Sulfolobus acidocaldarius Trm10 in complex with S-adenosylhomocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A7T PDB ENTRY 5A7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.4 M (NH4)2SO4, 0.1 M SODIUM ACETATE PH 4.5, 15-20 % PEG2000MME
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.14 α = 90 b = 101.09 β = 90 c = 66.81 γ = 90
Symmetry Space Group P 21 21 2
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 2013-05-01 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 2.5 48.1 99.1 0.01 13.26 5.4 22754 1.5
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 2.5 2.6 99.3 0.16 1.56 5.5
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 5A7T 2.5 48.09 21616 1138 99.11 0.23713 0.23439 0.2388 0.28923 0.2891 RANDOM 66.52
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] 2.61 -5.08 2.47
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 3.656 r_scbond_it 3.48 r_angle_other_deg 3.449 r_mcbond_it 2.389 r_mcbond_other 2.38 r_angle_refined_deg 1.492 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_other 0.007 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 3.656 r_scbond_it 3.48 r_angle_other_deg 3.449 r_mcbond_it 2.389 r_mcbond_other 2.38 r_angle_refined_deg 1.492 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4373 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing