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Crystal structure of the T. thermophilus dodecin R65A 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 0.4 M AMMONIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 1.88 34.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.585 α = 90 b = 67.585 β = 90 c = 169.188 γ = 120
Symmetry Space Group P 31 2 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 MARRESEARCH 2006-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 1.4 14.88 98 0.08 19.7 4.3 87239
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 1.4 1.44 96.2 0.3 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MOG 1.4 14.88 85624 1575 98 0.17 0.17 0.193 0.2378 RANDOM 12.91
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.589 r_dihedral_angle_4_deg 14.187 r_dihedral_angle_3_deg 11.11 r_dihedral_angle_1_deg 5.717 r_scangle_it 2.842 r_scbond_it 1.75 r_angle_refined_deg 1.427 r_mcangle_it 1.224 r_angle_other_deg 0.876 r_mcbond_it 0.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.589 r_dihedral_angle_4_deg 14.187 r_dihedral_angle_3_deg 11.11 r_dihedral_angle_1_deg 5.717 r_scangle_it 2.842 r_scbond_it 1.75 r_angle_refined_deg 1.427 r_mcangle_it 1.224 r_angle_other_deg 0.876 r_mcbond_it 0.654 r_symmetry_vdw_other 0.274 r_nbd_other 0.201 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.163 r_nbtor_other 0.083 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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 3159 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 493
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing