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Crystal structure of EcTrmB in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DXX PDB ENTRY 3DXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 283 15% PEG 3350 (w/v), 150 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.57 α = 90 b = 48.29 β = 90.52 c = 57.48 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 MAR CCD 165 mm 2007-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.000 BSRF 3W1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.58 19.97 34161
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3DXX 1.58 19.45 32460 1693 99.35 0.17517 0.17423 0.19285 0.201 RANDOM 15.611
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] 0.52 0.15 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.449 r_dihedral_angle_4_deg 11.266 r_dihedral_angle_3_deg 11.197 r_dihedral_angle_1_deg 5.117 r_scangle_it 2.142 r_scbond_it 1.353 r_angle_refined_deg 1.158 r_mcangle_it 0.791 r_mcbond_it 0.646 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.449 r_dihedral_angle_4_deg 11.266 r_dihedral_angle_3_deg 11.197 r_dihedral_angle_1_deg 5.117 r_scangle_it 2.142 r_scbond_it 1.353 r_angle_refined_deg 1.158 r_mcangle_it 0.791 r_mcbond_it 0.646 r_nbtor_refined 0.304 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.099 r_chiral_restr 0.073 r_bond_refined_d 0.007 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 1590 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling