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Crystal Structure of Agrobacterium tumefaciens NADQ, NAD complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 100 mM Bis-tris-propane, 250 mM sodium potassium tartrate, 24 % (w/v) PEG 3400
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.665 α = 90 b = 133.721 β = 101.047 c = 87.795 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-F 2020-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.19 86.17 98.7 0.06162 0.08714 0.984 10.27 2 67319 41.1
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 2.19 2.268 98.27 0.4347 0.6147 0.68 1.7 2
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 structure 2.19 86.17 1.34 67301 3402 98.7 0.2293 0.2278 0.2278 0.2588 0.2584 50.7
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 13.5192 f_angle_d 0.4551 f_chiral_restr 0.0376 f_plane_restr 0.0035 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8756 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing