☰ Navigation Tabs
The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 288 7% PEG 4000, 0.2M sodium acetate trihydrate, 0.3M Tris-HCl (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.401 α = 90 b = 132.422 β = 90 c = 196.013 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 110 CCD RAYONIX MX300HE 2014-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 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 2.76 30 99.9 0.993 12.3 4.5 67645
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 2.76 2.86 99.3 0.606 1.8 4.4
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 4TVU 2.76 30 62376 3231 96.72 0.1949 0.192 0.1985 0.251 0.2522 RANDOM 50.759
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] -0.56 0.92 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.483 r_dihedral_angle_4_deg 19.47 r_dihedral_angle_3_deg 16.007 r_dihedral_angle_1_deg 6.17 r_angle_refined_deg 1.298 r_angle_other_deg 1.238 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.483 r_dihedral_angle_4_deg 19.47 r_dihedral_angle_3_deg 16.007 r_dihedral_angle_1_deg 6.17 r_angle_refined_deg 1.298 r_angle_other_deg 1.238 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16951 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing