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Uroporphyrinogen Decarboxylase single mutant D86E 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 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 2.4 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.111 α = 90 b = 103.111 β = 90 c = 73.313 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 1.9 20 98 0.134 0.134 9 6.2 35021 35021
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 1.9 1.97 95 0.399 0.399 2.5 6.2
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 1.9 19.5 35021 33590 1403 100 0.15203 0.15203 0.15052 0.1651 0.1869 0.1929 RANDOM 16.723
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] -0.56 -0.28 -0.56 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.515 r_scangle_it 4.745 r_scbond_it 2.873 r_mcangle_it 1.769 r_angle_refined_deg 1.63 r_mcbond_it 0.994 r_angle_other_deg 0.933 r_symmetry_vdw_other 0.351 r_nbd_other 0.25 r_nbd_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.515 r_scangle_it 4.745 r_scbond_it 2.873 r_mcangle_it 1.769 r_angle_refined_deg 1.63 r_mcbond_it 0.994 r_angle_other_deg 0.933 r_symmetry_vdw_other 0.351 r_nbd_other 0.25 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.208 r_symmetry_vdw_refined 0.186 r_chiral_restr 0.108 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002 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 2803 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement