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Uroporphyrinogen Decarboxylase single mutant D86G in complex with coproporphyrinogen-III
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 PBG, PBG-D and U3S were added to the protein solution in an anaerobic
chamber. URO-D was active under these conditions, converting
uro'gen-III to cop'gen-III. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.36 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.68 α = 90 b = 102.68 β = 90 c = 73.13 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 1.7 87.71 96 0.096 0.096 13 4.9 47218 47218
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 1.7 1.76 88 0.232 0.232 2.7 4.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1URO 1.7 87.71 47218 45924 1187 95.76 0.17019 0.17019 0.16944 0.20004 0.2222 RANDOM 22.484
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] -1.05 -0.53 -1.05 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.615 r_scangle_it 4.062 r_scbond_it 2.515 r_mcangle_it 1.641 r_angle_refined_deg 1.547 r_mcbond_it 0.959 r_angle_other_deg 0.887 r_symmetry_hbond_refined 0.352 r_symmetry_vdw_refined 0.334 r_symmetry_vdw_other 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.615 r_scangle_it 4.062 r_scbond_it 2.515 r_mcangle_it 1.641 r_angle_refined_deg 1.547 r_mcbond_it 0.959 r_angle_other_deg 0.887 r_symmetry_hbond_refined 0.352 r_symmetry_vdw_refined 0.334 r_symmetry_vdw_other 0.316 r_nbd_other 0.24 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.098 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2794 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement