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resting state of homogentisate 1,2-dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EYB PDB ENTRY 1EYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 VAPOUR DIFFUSION(1:1): 17 % PEG 3350, 0.02 M NAK PHOSPHATE, 0.1 M BIS-TRIS PROPANE PH 8.0, 1 MM TCEP 15 MG/ML PROTEIN
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.737 α = 87.46 b = 93.901 β = 80.45 c = 162.81 γ = 68.33
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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 34 94 0.09 10.8 2.9 359608 2 16.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 80 0.44 2.38 2.7
Refinement Statistics Diffraction ID Structure Solution 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 MOLECULAR REPLACEMENT PDB ENTRY 1EYB 1.95 33.936 1.99 351605 17580 94.82 0.1958 0.1925 0.1905 0.2573 0.2551
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] -0.431 0.5355 0.7097 1.5511 0.0005 1.2577
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.053 f_angle_d 1.109 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39464 Nucleic Acid Atoms Solvent Atoms 5676 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing