☰ Navigation Tabs
Crystal structure of Pyrobaculum aerophilum L7Ae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other P. islandicum L7Ae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 Crystals were grown by vapor diffusion in 100 mM sodium acetate, pH 4.6, 2 M ammonium sulfate at 295 K.
Crystals were cryo-protected in 100 mM sodium acetate, pH 4.6, 2 M ammonium sulfate, 20% (v/v) glycerol and flash frozen with liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 3.13 60.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.513 α = 90 b = 94.89 β = 93.103 c = 128.318 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 RAYONIX MX-300 Mirrors 2016-03-16 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 1.45 19.95 85.5 0.052 0.058 0.998 13.8 4.6 239142
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 1.45 1.53 28.7 0.775 0.873 0.699 1.7 4.7
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 1.452 19.95 239114 12016 85.467 0.171 0.1704 0.1682 0.1865 0.1847 21.51
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] -1.638 -1.814 1.395 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.812 r_dihedral_angle_3_deg 11.35 r_dihedral_angle_2_deg 10.748 r_lrange_it 6.099 r_lrange_other 6.099 r_dihedral_angle_1_deg 5.699 r_scangle_it 3.634 r_scangle_other 3.634 r_scbond_it 2.42 r_scbond_other 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.812 r_dihedral_angle_3_deg 11.35 r_dihedral_angle_2_deg 10.748 r_lrange_it 6.099 r_lrange_other 6.099 r_dihedral_angle_1_deg 5.699 r_scangle_it 3.634 r_scangle_other 3.634 r_scbond_it 2.42 r_scbond_other 2.42 r_mcangle_other 2.08 r_mcangle_it 2.078 r_angle_refined_deg 1.676 r_mcbond_it 1.272 r_mcbond_other 1.232 r_angle_other_deg 0.567 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_refined 0.188 r_symmetry_nbd_other 0.186 r_nbd_other 0.181 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.112 r_ncsr_local_group_6 0.101 r_ncsr_local_group_15 0.101 r_ncsr_local_group_17 0.099 r_ncsr_local_group_22 0.099 r_ncsr_local_group_4 0.098 r_ncsr_local_group_20 0.098 r_ncsr_local_group_21 0.098 r_ncsr_local_group_5 0.097 r_ncsr_local_group_7 0.097 r_ncsr_local_group_12 0.096 r_ncsr_local_group_19 0.096 r_ncsr_local_group_16 0.095 r_ncsr_local_group_18 0.095 r_ncsr_local_group_10 0.092 r_ncsr_local_group_11 0.092 r_chiral_restr 0.089 r_ncsr_local_group_13 0.089 r_ncsr_local_group_28 0.079 r_ncsr_local_group_23 0.078 r_ncsr_local_group_26 0.078 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_3 0.076 r_ncsr_local_group_14 0.076 r_ncsr_local_group_25 0.073 r_ncsr_local_group_8 0.072 r_ncsr_local_group_9 0.071 r_ncsr_local_group_1 0.068 r_ncsr_local_group_24 0.067 r_ncsr_local_group_2 0.059 r_ncsr_local_group_27 0.054 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8899 Nucleic Acid Atoms Solvent Atoms 954 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing