☰ Navigation Tabs
Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum
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 0.2 M AMMONIUM SULFATE, 22% PEG 3350,
0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.57 α = 90 b = 54.484 β = 90 c = 83.177 γ = 90
Symmetry Space Group P 21 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 100 CCD RAYONIX MX300HE 2016-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.65 89 99.8 0.999 24.4 6.9 97625
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 1.65 1.71 0.77
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 1.65 88.79 91118 4701 97.91 0.1635 0.1621 0.1744 0.1909 0.2011 RANDOM 16.977
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] -0.1 0.19 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.738 r_dihedral_angle_4_deg 18.223 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.362 r_angle_refined_deg 1.359 r_angle_other_deg 0.922 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.738 r_dihedral_angle_4_deg 18.223 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.362 r_angle_refined_deg 1.359 r_angle_other_deg 0.922 r_chiral_restr 0.082 r_bond_refined_d 0.009 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 6217 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction