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Crystal Structure of Uroporphyrinogen Decarboxylase from Bacillus subtilis
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 VAPOR DIFFUSION, HANGING DROP 5.6 293 25% PEG 2000, 100mM citrate, 160mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.612 α = 68.68 b = 80.41 β = 89.64 c = 90.94 γ = 80.82
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 MAR CCD 165 mm 2003-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.1 BSRF 3W1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 30 96.2 0.063 67725 65152 1.6 1.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.36 96.2 0.406 2.4
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1URO 2.3 30 64278 61835 3316 96.23 0.205 0.20013 0.19744 0.2335 0.25125 0.2761 RANDOM 53.559
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] -0.53 0.11 -0.29 -0.85 1.36 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.337 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 16.357 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.003 r_angle_refined_deg 1.29 r_scbond_it 1.272 r_mcangle_it 0.875 r_mcbond_it 0.515 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.337 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 16.357 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.003 r_angle_refined_deg 1.29 r_scbond_it 1.272 r_mcangle_it 0.875 r_mcbond_it 0.515 r_nbtor_refined 0.3 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.092 r_symmetry_hbond_refined 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10772 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection AUTOMAR data reduction CCP4 data scaling AMoRE phasing