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Crystal structure of the T. thermophilus dodecin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MOG PDB ENTRY 1MOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M SODIUM CITRATE, 0.1 M TRIS/HCL, PH 7.5, 25% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.2 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.481 α = 90 b = 98.038 β = 90 c = 137.595 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2003-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.6 24.8 76 0.08 19 2.75 22085
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 2.59 2.73 0.24 3.9
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 1MOG 2.59 24.76 20911 1125 76.2 0.22 0.219 0.2193 0.244 0.242 RANDOM 52.04
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] 0.22 0.12 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.361 r_dihedral_angle_3_deg 15.585 r_dihedral_angle_4_deg 12.258 r_dihedral_angle_1_deg 5.662 r_scangle_it 1.738 r_angle_refined_deg 1.277 r_scbond_it 0.993 r_angle_other_deg 0.801 r_mcangle_it 0.579 r_symmetry_hbond_refined 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.361 r_dihedral_angle_3_deg 15.585 r_dihedral_angle_4_deg 12.258 r_dihedral_angle_1_deg 5.662 r_scangle_it 1.738 r_angle_refined_deg 1.277 r_scbond_it 0.993 r_angle_other_deg 0.801 r_mcangle_it 0.579 r_symmetry_hbond_refined 0.527 r_mcbond_it 0.522 r_symmetry_vdw_other 0.301 r_symmetry_vdw_refined 0.257 r_nbd_other 0.192 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.183 r_nbd_refined 0.179 r_nbtor_other 0.08 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 6372 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 804
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing