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Uroporphyrinogen Decarboxylase single mutant D86G in complex with coproporphyrinogen-I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URO PDB ENTRY 1URO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.5 294 PBG and PBG-D were added to the protein solution in an anaerobic
chamber. URO-D was active under these conditions, converting uro'gen-I
to cop'gen-I. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.31 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.947 α = 90 b = 102.947 β = 90 c = 72.585 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 1.65 87.71 97 0.072 0.072 10 5 51831 51831
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 1.65 1.71 80 0.236 0.236 1.8 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1URO 1.65 87.71 51831 50541 1290 96.64 0.16321 0.16321 0.16255 0.19 0.2431 RANDOM 23.05
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 -0.76 -1.53 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.584 r_scangle_it 4.311 r_scbond_it 2.602 r_angle_refined_deg 1.845 r_mcangle_it 1.734 r_mcbond_it 0.944 r_angle_other_deg 0.891 r_symmetry_vdw_refined 0.396 r_symmetry_vdw_other 0.357 r_nbd_other 0.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.584 r_scangle_it 4.311 r_scbond_it 2.602 r_angle_refined_deg 1.845 r_mcangle_it 1.734 r_mcbond_it 0.944 r_angle_other_deg 0.891 r_symmetry_vdw_refined 0.396 r_symmetry_vdw_other 0.357 r_nbd_other 0.244 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.21 r_symmetry_hbond_refined 0.181 r_chiral_restr 0.094 r_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2794 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement