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Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.
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 VAPOUR DIFFUSION (1:1 MIX): 17% PEG 3350, 0.02 M NAK PHOSPHATE AND 0.1 M BIS-TRIS PROPANE PH 8.0, 1MM TCEP, 2 MICROM HOMOGENTISATE, 15 MG/ML PROTEIN
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.737 α = 87.62 b = 93.857 β = 80.39 c = 163.438 γ = 68.29
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 1.7 35 94.9 0.08 9.85 2.9 532721 2 16.64
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 1.7 35 91.1 0.53 2.13 2.9
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 PDB ENTRY 1EYB 1.7 34.37 532705 26681 94.91 0.2055 0.2031 0.2249 0.2518 0.2247 RANDOM 18.78
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] 0.8778 -1.1551 1.0538 1.7939 -0.0271 -2.6717
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.15 t_omega_torsion 3.68 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.15 t_omega_torsion 3.68 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39964 Nucleic Acid Atoms Solvent Atoms 5701 Heterogen Atoms 169
Software Software Software Name Purpose BUSTER refinement PHASER phasing