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Uroporphyrinogen Decarboxylase with mutation D86N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.5 294 The crystal trial was conducted in an anaerobic chamber, with PBG,
PBG-D added to the solution. These conditions are conducive to
formation of an enzyme product complex, as the enzyme is typically
active under these conditions (see related strcuture 1R3Q). There is
not a ligand bound in this structure. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.37 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.735 α = 90 b = 102.735 β = 90 c = 73.426 γ = 120
Symmetry Space Group P 31 2 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 IMAGE PLATE RIGAKU RAXIS IIC 2003-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 87.71 96 0.083 0.083 9 5 36928 36928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.92 80 0.437 0.437 2.8 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1URO 1.85 87.71 36928 35762 1122 95.81 0.16212 0.16212 0.16117 0.1688 0.19242 0.2009 RANDOM 20.283
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] -1.53 -0.77 -1.53 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.737 r_scangle_it 5.177 r_scbond_it 3.091 r_mcangle_it 2.019 r_angle_refined_deg 1.69 r_mcbond_it 1.119 r_angle_other_deg 0.961 r_symmetry_vdw_refined 0.42 r_symmetry_vdw_other 0.353 r_nbd_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.737 r_scangle_it 5.177 r_scbond_it 3.091 r_mcangle_it 2.019 r_angle_refined_deg 1.69 r_mcbond_it 1.119 r_angle_other_deg 0.961 r_symmetry_vdw_refined 0.42 r_symmetry_vdw_other 0.353 r_nbd_other 0.25 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.205 r_symmetry_hbond_refined 0.194 r_chiral_restr 0.106 r_nbtor_other 0.087 r_bond_refined_d 0.02 r_gen_planes_other 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2989 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement