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Structure of universal stress protein from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M BIS-TRIS PH5.5, 0.2M AMMONIUM
ACETATE, 25%PEG3350.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.174 α = 90 b = 99.158 β = 92.38 c = 57.387 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 SBC-3 MIRROR 2008-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 50 99.9 0.066 0.074 0.034 8.4 4.5 38249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.762 0.867 0.408 0.746 4.3
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 3DLO 1.9 32.01 33097 1666 91.42 0.16936 0.16743 0.1806 0.20736 0.2144 RANDOM 29.148
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] 0.6 -1.17 -0.97 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.268 r_scbond_other 18.115 r_scbond_it 18.095 r_scangle_other 17.509 r_dihedral_angle_4_deg 17.041 r_long_range_B_other 16.945 r_long_range_B_refined 16.944 r_dihedral_angle_3_deg 13.481 r_mcangle_it 8.599 r_mcangle_other 8.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.268 r_scbond_other 18.115 r_scbond_it 18.095 r_scangle_other 17.509 r_dihedral_angle_4_deg 17.041 r_long_range_B_other 16.945 r_long_range_B_refined 16.944 r_dihedral_angle_3_deg 13.481 r_mcangle_it 8.599 r_mcangle_other 8.598 r_mcbond_it 7.973 r_mcbond_other 7.732 r_dihedral_angle_1_deg 6.365 r_angle_refined_deg 1.114 r_angle_other_deg 0.823 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4125 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-3000 data reduction