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Crystal structure of E.coli TrmJ in complex with S-adenosyl-L- homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CND PDB ENTRY 4CND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.02M NA/KPO4, 0.1M MES PH6.5, 20% PEG3350, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.05 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.44 α = 90 b = 72.85 β = 107.75 c = 55.54 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 PIXEL DECTRIS PILATUS 6M 2012-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.9 20 99.9 0.05 17.2 4.2 24619 3.4
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 1.9 2 91.9 0.44 3.4 3.4
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 4CND 1.9 19.58 23340 1242 96.45 0.18236 0.18 0.1866 0.22753 0.2311 RANDOM 39.423
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] -1.17 -0.63 -0.2 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.337 r_dihedral_angle_4_deg 15.92 r_dihedral_angle_3_deg 13.501 r_dihedral_angle_1_deg 6.329 r_angle_other_deg 3.574 r_scbond_it 2.512 r_mcangle_it 2.4 r_mcbond_it 1.769 r_mcbond_other 1.739 r_angle_refined_deg 1.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.337 r_dihedral_angle_4_deg 15.92 r_dihedral_angle_3_deg 13.501 r_dihedral_angle_1_deg 6.329 r_angle_other_deg 3.574 r_scbond_it 2.512 r_mcangle_it 2.4 r_mcbond_it 1.769 r_mcbond_other 1.739 r_angle_refined_deg 1.495 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_other 0.015 r_gen_planes_refined 0.01 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2481 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing