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Crystal structure of E.coli TrmJ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ILK PDB ENTRY 3ILK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.02M NA/KPO4, 0.1M MES PH6.5, 19% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.05 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.4 α = 90 b = 73.03 β = 105.13 c = 53.33 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 ADSC QUANTUM 210 2012-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.5 40 97.5 0.06 23.2 7.2 49018 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 1.5 1.6 80.3 0.88 2 5.4
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 3ILK 1.5 40.93 46569 2451 97.57 0.19696 0.1953 0.2026 0.22822 0.2327 RANDOM 20.045
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] -0.39 -0.13 -0.45 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.083 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 6.319 r_angle_other_deg 3.647 r_scbond_it 3.038 r_mcangle_it 2.818 r_mcbond_it 2.082 r_mcbond_other 2.079 r_angle_refined_deg 1.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.083 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 6.319 r_angle_other_deg 3.647 r_scbond_it 3.038 r_mcangle_it 2.818 r_mcbond_it 2.082 r_mcbond_other 2.079 r_angle_refined_deg 1.712 r_chiral_restr 0.115 r_gen_planes_other 0.019 r_bond_refined_d 0.015 r_gen_planes_refined 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2478 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing