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Crystal structure of EcTrmB in complex with SAM
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% (w/v) PEG 3350, 150mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.04 α = 90 b = 46.76 β = 90.4 c = 58.13 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 1.5 17.98 39292
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 3DXX 1.5 17.9 37308 1980 98.8 0.15526 0.1537 0.1518 0.18508 0.1827 RANDOM 16.06
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] -0.04 -0.04 0.16 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.401 r_sphericity_free 19.374 r_dihedral_angle_3_deg 11.574 r_dihedral_angle_4_deg 9.446 r_sphericity_bonded 6.528 r_dihedral_angle_1_deg 5.099 r_scangle_it 3.173 r_scbond_it 2.154 r_mcangle_it 1.583 r_rigid_bond_restr 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.401 r_sphericity_free 19.374 r_dihedral_angle_3_deg 11.574 r_dihedral_angle_4_deg 9.446 r_sphericity_bonded 6.528 r_dihedral_angle_1_deg 5.099 r_scangle_it 3.173 r_scbond_it 2.154 r_mcangle_it 1.583 r_rigid_bond_restr 1.5 r_angle_refined_deg 1.256 r_mcbond_it 0.947 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.089 r_xyhbond_nbd_refined 0.084 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1653 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing