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Anaerobic complex of urate oxidase with uric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ICQ PDB ENTRY 2ICQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 liquide diffusion in gel phase 10.5 290 SOLUTION A (0.1 ML): 50MM TRIS BUFFER, SATURATED WITH ACID URIC, 10% PEG 8000, PH 10.5, 0.5 MM AGAROSE IN CAPPILARY (HALF FILLING), SET AS A GEL (BY COOLING FROM 323 K TO ROOM TEMP).
SOLUTION B (0.1 ML): 20 MG/ML PROTEIN, SAME BUFFER, SET IN CONTACT WITHIN THE CAPILLARY WITH SOL.A. CRYSTALS DEVELOP IN THE GEL PHASE BY SLOW DIFFUSION.
ALL SOLUTION DEGASED, CRYSTALLIZATIONS UNDER ARGON ATMOSPHERE (ANAEROBIC CONDITIONS), liquide diffusion in gel phase, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.9 57.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.853 α = 90 b = 96.29 β = 90 c = 105.737 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 CCD ADSC QUANTUM 315r BENT MIRROR 2008-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A
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 1.5 26.7 99.4 0.068 18.1 4.6 64921 2 4
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 1.5 1.55 86.17 0.232 3.9 3.9 6068
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS FREE R PDB ENTRY 2ICQ 1.5 10 4 2 64760 60335 3883 99.4 0.2302 0.2277 0.2201 0.2442 0.2492 0.2339 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 9 2314 2625
RMS Deviations Key Refinement Restraint Deviation s_angle_d 0.076 s_non_zero_chiral_vol 0.057 s_zero_chiral_vol 0.05 s_anti_bump_dis_restr 0.049 s_bond_d 0.03 s_from_restr_planes 0.027 s_similar_dist s_rigid_bond_adp_cmpnt s_similar_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2362 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 13
Software Software Software Name Purpose ADSC data collection SHELXL-97 refinement MOSFLM data reduction SCALA data scaling TRUNCATE data scaling