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Crystal Structure of Agrobacterium tumefaciens NADQ, ATP complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 100 mM Bis-tris-propane, pH 7.0, 250 mM sodium potassium tartrate, 24 % (w/v) PEG 3400
Crystal Properties Matthews coefficient Solvent content 2.12 41.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.92 α = 90 b = 132.57 β = 100.158 c = 86.85 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9797 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.18 51.84 99.5 0.105 0.114 0.998 12.6 6.5 66672 37.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.22 99.5 0.887 0.964 0.696 2.1 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE native form 2.18 51.84 1.34 66667 3386 99.55 0.2318 0.2298 0.2299 0.2694 0.2691 44.59
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.3419 f_angle_d 0.4323 f_chiral_restr 0.0362 f_plane_restr 0.0035 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9422 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing