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High resolution structure of TtrD from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IDG PDB ENTRY 2IDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M SODIUM FORMATE, 20% PEG 3350, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.763 α = 90 b = 52.537 β = 91.26 c = 64.947 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 CCD 2010-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.35 64.69 96.9 0.05 17.6 6.9 89700 14.78
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 1.35 1.42 94.9 0.49 4.2 6.3
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 2IDG 1.35 64.93 85158 4523 96.6 0.15248 0.15116 0.1603 0.17751 0.1845 RANDOM 16.751
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] 0.03 0.17 0.2 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.876 r_dihedral_angle_4_deg 21.578 r_dihedral_angle_3_deg 13.372 r_scangle_it 7.335 r_scbond_it 5.082 r_dihedral_angle_1_deg 4.518 r_mcangle_it 3.598 r_mcbond_it 2.4 r_rigid_bond_restr 1.34 r_angle_refined_deg 1.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.876 r_dihedral_angle_4_deg 21.578 r_dihedral_angle_3_deg 13.372 r_scangle_it 7.335 r_scbond_it 5.082 r_dihedral_angle_1_deg 4.518 r_mcangle_it 3.598 r_mcbond_it 2.4 r_rigid_bond_restr 1.34 r_angle_refined_deg 1.277 r_mcbond_other 0.953 r_angle_other_deg 0.895 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing