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Uroporphyrinogen Decarboxylase G168R single mutant apo-enzyme
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 VAPOR DIFFUSION, SITTING DROP 7 298 Protein 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), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.236 α = 90 b = 103.236 β = 90 c = 72.398 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 II Yale focusing mirrors 2003-09-16 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 2 40 98.9 0.109 10.1 30032
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) 2 2.07 99 0.497 2974
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 1URO 2 40 30010 1199 98.63 0.176 0.174 0.188 0.222 0.2324 RANDOM 30.153
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] -2.36 -1.18 -2.36 3.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 15.783 r_dihedral_angle_1_deg 6.206 r_scangle_it 3.17 r_scbond_it 2.233 r_mcangle_it 1.541 r_angle_refined_deg 1.416 r_mcbond_it 1.403 r_angle_other_deg 0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 15.783 r_dihedral_angle_1_deg 6.206 r_scangle_it 3.17 r_scbond_it 2.233 r_mcangle_it 1.541 r_angle_refined_deg 1.416 r_mcbond_it 1.403 r_angle_other_deg 0.874 r_symmetry_vdw_other 0.303 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.203 r_mcbond_other 0.201 r_nbd_other 0.185 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.158 r_chiral_restr 0.089 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2896 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction