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Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-I
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 Crystallization of URO-D in complex with coproporphyrinogen required
crystallization in an anaerobic chamber with PBG and PBG-D added to
the solution for the generation of uroporphyrinogen in-situ. URO-D
was active under these conditions, creating coproporphyrinogen. 1.5 M
citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.5 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.93 α = 90 b = 102.93 β = 90 c = 74.51 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 CCD ADSC QUANTUM 4 2001-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.1000 ALS 5.0.2
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 30 100 0.092 0.092 13 5.5 50593 50593
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 1.76 100 0.485 0.485 2.8 5.5
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 1.7 87.71 50593 48908 1245 99.54 0.16749 0.16749 0.16684 0.1794 0.19248 0.2084 RANDOM 25.44
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] -1.27 -0.63 -1.27 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.412 r_scangle_it 5 r_scbond_it 2.976 r_mcangle_it 1.911 r_angle_refined_deg 1.633 r_mcbond_it 1.042 r_angle_other_deg 0.884 r_symmetry_vdw_other 0.337 r_nbd_other 0.242 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.412 r_scangle_it 5 r_scbond_it 2.976 r_mcangle_it 1.911 r_angle_refined_deg 1.633 r_mcbond_it 1.042 r_angle_other_deg 0.884 r_symmetry_vdw_other 0.337 r_nbd_other 0.242 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.096 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2802 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 51
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement