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Crystal structure of the T. thermophilus dodecin R45A mutant
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 0.1 M AMMONIUM SULFATE, 0.05 M SODIUM CACODYLATE, PH 6.5 AND 15% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.7 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.294 α = 90 b = 68.494 β = 90 c = 229.891 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 11 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2005-03-22 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 2.58 25 95.9 0.09 13.2 3.7 32742
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 2.66 0.24 3.5
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 25 31678 1018 96.1 0.207 0.206 0.2276 0.234 0.2506 RANDOM 30.33
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] 2.85 -1.6 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.487 r_dihedral_angle_3_deg 17.381 r_dihedral_angle_4_deg 15.232 r_dihedral_angle_1_deg 10.928 r_scangle_it 4.544 r_scbond_it 3.049 r_mcangle_it 1.86 r_mcbond_it 1.528 r_angle_refined_deg 1.002 r_angle_other_deg 0.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.487 r_dihedral_angle_3_deg 17.381 r_dihedral_angle_4_deg 15.232 r_dihedral_angle_1_deg 10.928 r_scangle_it 4.544 r_scbond_it 3.049 r_mcangle_it 1.86 r_mcbond_it 1.528 r_angle_refined_deg 1.002 r_angle_other_deg 0.572 r_symmetry_vdw_other 0.396 r_symmetry_vdw_refined 0.255 r_nbd_other 0.228 r_nbd_refined 0.22 r_nbtor_refined 0.193 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.156 r_nbtor_other 0.087 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 6336 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 891
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing