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crystal structure of GDSL esterase from Geobacillus thermodenitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.1 60.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.424 α = 90 b = 106.424 β = 90 c = 128.643 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MAR CCD 130 mm 2020-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.2 0.118 0.024 0.968 1.9 20 22907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 1.144 0.227 0.933 1.5
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 1U8U 2.62 32.5 21586 1149 99.21 0.2464 0.2447 0.243 0.2783 0.2716 RANDOM 70
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] 1.18 1.18 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.266 r_dihedral_angle_3_deg 16.69 r_dihedral_angle_4_deg 16.05 r_dihedral_angle_1_deg 5.978 r_angle_refined_deg 1.348 r_angle_other_deg 1.339 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.266 r_dihedral_angle_3_deg 16.69 r_dihedral_angle_4_deg 16.05 r_dihedral_angle_1_deg 5.978 r_angle_refined_deg 1.348 r_angle_other_deg 1.339 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3242 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing