☰ Navigation Tabs
Crystal structure of TxGH116 E441G nucleophile mutant from Thermoanaerobacterium xylanolyticum with autocondensation products from alpha-fluoroglucoside.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 0.24 M AMMONIUM SULFATE, 20% PEG 3350, 0.1 M MES, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.214 α = 90 b = 54.602 β = 90 c = 164.55 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 ADSC QUANTUM 315r 2018-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.78 35 99.4 0.998 23 4.8 155241
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 1.78 1.84 0.823
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 5BVU 1.78 35 144496 7479 97.75 0.1592 0.1577 0.1684 0.1879 0.1951 RANDOM 22.459
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] -0.17 0.1 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.288 r_dihedral_angle_4_deg 17.745 r_dihedral_angle_3_deg 12.921 r_dihedral_angle_1_deg 6.412 r_angle_refined_deg 1.379 r_angle_other_deg 0.924 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.288 r_dihedral_angle_4_deg 17.745 r_dihedral_angle_3_deg 12.921 r_dihedral_angle_1_deg 6.412 r_angle_refined_deg 1.379 r_angle_other_deg 0.924 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12449 Nucleic Acid Atoms Solvent Atoms 1280 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction