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Crystal structure of Thermotoga maritima mutant D89K/D253K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 0.2 M Mg(HCO2)2, 0.1 M MES, pH 6.0, 25% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.125 α = 90 b = 104.488 β = 106.13 c = 122.821 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 315 2014-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.05 47.8 99.2 0.083 0.999 11.3 3.8 56456
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 3.05 3.23 98.1 1.544 1 3.8
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 2IUB 3.05 47.77 53629 2823 99.29 0.24774 0.24552 0.2294 0.29062 0.2714 RANDOM 126.119
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] -3.68 -6.18 1.22 3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.535 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 15.859 r_long_range_B_refined 15.087 r_long_range_B_other 15.087 r_dihedral_angle_1_deg 9.793 r_scangle_other 9.146 r_mcangle_it 8.412 r_mcangle_other 8.411 r_scbond_it 5.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.535 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 15.859 r_long_range_B_refined 15.087 r_long_range_B_other 15.087 r_dihedral_angle_1_deg 9.793 r_scangle_other 9.146 r_mcangle_it 8.412 r_mcangle_other 8.411 r_scbond_it 5.572 r_scbond_other 5.572 r_mcbond_other 5.252 r_mcbond_it 5.251 r_angle_refined_deg 1.099 r_angle_other_deg 0.831 r_chiral_restr 0.056 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13335 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHASER phasing XDS data reduction