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Crystal structure of Pyrobaculum islandicum L7Ae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 303 Crystals were grown by vapor diffusion in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 at 303 K.
Crystals were cryo-protected in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 22.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 and flash frozen with liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.852 α = 87.134 b = 60 β = 75.531 c = 60.71 γ = 84.241
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 RAYONIX MX-300 Mirrors 2016-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 0.998 19.89 70.9 0.045 0.027 0.998 14.3 3.9 203846
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.998 1.07 17.6 0.922 0.548 0.602 1.3 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.998 19.89 203839 9969 70.984 0.137 0.1363 0.1352 0.151 0.1495 11.334
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] -0.665 0.714 0.105 -0.625 -0.666 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.717 r_dihedral_angle_3_deg 11.234 r_lrange_it 11.082 r_lrange_other 11.081 r_dihedral_angle_2_deg 7.093 r_dihedral_angle_1_deg 5.752 r_scangle_it 5.296 r_scangle_other 5.296 r_mcangle_other 4.163 r_mcangle_it 4.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.717 r_dihedral_angle_3_deg 11.234 r_lrange_it 11.082 r_lrange_other 11.081 r_dihedral_angle_2_deg 7.093 r_dihedral_angle_1_deg 5.752 r_scangle_it 5.296 r_scangle_other 5.296 r_mcangle_other 4.163 r_mcangle_it 4.162 r_scbond_it 3.435 r_scbond_other 3.434 r_rigid_bond_restr 2.542 r_mcbond_it 2.541 r_mcbond_other 2.531 r_angle_refined_deg 1.453 r_angle_other_deg 0.497 r_symmetry_nbd_refined 0.244 r_xyhbond_nbd_refined 0.229 r_nbd_refined 0.224 r_symmetry_nbd_other 0.188 r_nbd_other 0.172 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.148 r_chiral_restr 0.078 r_symmetry_metal_ion_refined 0.077 r_symmetry_nbtor_other 0.076 r_metal_ion_refined 0.05 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4343 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing