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Crystal structure of hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 293.15 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH6.5, 30% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 111.628 β = 90 c = 114.885 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 293.15 PIXEL DECTRIS EIGER X 16M 2023-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.667 47.4802 99.58 0.019 0.027 0.019 0.999 16.2 2 88855 26.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 47.48 99.58 0.999
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 1.67 47.48 88429 4453 99.723 0.171 0.1679 0.2121 0.2253 0.2563 20.086
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] -0.096 -2.162 2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.265 r_dihedral_angle_3_deg 13.025 r_lrange_it 13.013 r_scangle_it 11.261 r_dihedral_angle_2_deg 10.557 r_scbond_it 8.431 r_rigid_bond_restr 7.482 r_mcangle_it 7.436 r_dihedral_angle_1_deg 5.999 r_mcbond_it 5.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.265 r_dihedral_angle_3_deg 13.025 r_lrange_it 13.013 r_scangle_it 11.261 r_dihedral_angle_2_deg 10.557 r_scbond_it 8.431 r_rigid_bond_restr 7.482 r_mcangle_it 7.436 r_dihedral_angle_1_deg 5.999 r_mcbond_it 5.585 r_angle_refined_deg 2.252 r_nbtor_refined 0.317 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.174 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5841 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing Aimless data scaling