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Crystal structure of the extremely thermostable Aeropyrum pernix L7Ae multifunctional protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 4000, 10% Isopropanol, 100 mM HEPES-KOH, pH 7.5, 1 mM ZnCl2 mixed 1:2 with 500 microMolar L7Ae protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.054 α = 90 b = 49.188 β = 90 c = 65.048 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 100 CCD RIGAKU SATURN 92 Osmic Confocal Blue Max-Flux 2004-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 1.54 65.05 81.5 0.025 23.7 2.45 34157 13926 3 17.53
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 1.54 1.6 15.8 0.289 2.3 1.08 1678
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XBI 1.56 32.44 1 13760 13737 695 99.08 0.177 0.177 0.174 0.1888 0.226 0.2325 RANDOM 15.807
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] 0.02 -0.56 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.439 r_dihedral_angle_4_deg 15.801 r_sphericity_free 11.286 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 5.482 r_scangle_it 4.634 r_scbond_it 3.161 r_sphericity_bonded 3.042 r_rigid_bond_restr 2.132 r_mcangle_it 1.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.439 r_dihedral_angle_4_deg 15.801 r_sphericity_free 11.286 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 5.482 r_scangle_it 4.634 r_scbond_it 3.161 r_sphericity_bonded 3.042 r_rigid_bond_restr 2.132 r_mcangle_it 1.822 r_mcbond_it 1.542 r_angle_refined_deg 1.419 r_angle_other_deg 0.928 r_mcbond_other 0.431 r_symmetry_vdw_other 0.363 r_nbd_refined 0.21 r_nbd_other 0.193 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.085 r_nbtor_other 0.082 r_symmetry_vdw_refined 0.049 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 957 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction CrystalClear data scaling