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Uroporphyrinogen Decarboxylase G168R single mutant enzyme in complex with coproporphyrinogen-III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Protien at 6.5 mg/ml in 50mM Tris, pH 7.5, 1mM BME was mixed 5 parts to 3 parts of precipitant (1.7M citrate, pH 7.0) and equilibrated by sitting drop vapor diffusion against a well of precipitant., VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.037 α = 90 b = 103.037 β = 90 c = 71.865 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 Yale focusing mirrors 2003-09-19 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) 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 30 93.5 0.078 11.3 32683
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 82 0.442 2806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 MOLECULAR REPLACEMENT THROUGHOUT 1ry3 1.9 30 32682 1135 93.54 0.164 0.162 0.1638 0.199 0.2024 RANDOM 27.004
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] -1.51 -0.76 -1.51 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 13.701 r_dihedral_angle_1_deg 5.736 r_scangle_it 3.625 r_scbond_it 2.245 r_mcangle_it 1.476 r_angle_refined_deg 1.41 r_mcbond_it 0.904 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 13.701 r_dihedral_angle_1_deg 5.736 r_scangle_it 3.625 r_scbond_it 2.245 r_mcangle_it 1.476 r_angle_refined_deg 1.41 r_mcbond_it 0.904 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing