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Uroporphyrinogen Decarboxylase Y164F mutant 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 2.4 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.035 α = 90 b = 103.035 β = 90 c = 73.646 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 IV 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 99 0.071 0.071 12 5.9 49087 49087
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 99 0.39 0.39 1.8 5.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1URO 1.7 87.71 49087 47852 1226 98.66 0.1583 0.1583 0.15753 0.172 0.18887 0.2007 RANDOM 23.551
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] -1.01 -0.5 -1.01 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.09 r_scangle_it 4.288 r_scbond_it 2.597 r_mcangle_it 1.689 r_angle_refined_deg 1.549 r_mcbond_it 0.922 r_angle_other_deg 0.911 r_symmetry_vdw_other 0.328 r_nbd_other 0.244 r_symmetry_vdw_refined 0.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.09 r_scangle_it 4.288 r_scbond_it 2.597 r_mcangle_it 1.689 r_angle_refined_deg 1.549 r_mcbond_it 0.922 r_angle_other_deg 0.911 r_symmetry_vdw_other 0.328 r_nbd_other 0.244 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.211 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.095 r_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.01 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2797 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement