☰ Navigation Tabs
The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S4D PDB ENTRY 1S4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 PROTEIN WAS CRYSTALLIZED FROM 24% PEG 6000, 0.1 M TRIS PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.9 α = 90 b = 115.1 β = 90 c = 76.8 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU CCD MIRRORS 2009-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 46.31 99.8 0.04 20.19 4.4 19360 2 35.1
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 2 2.05 99.9 0.59 2.58 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1S4D 2 26.915 2 18294 915 98.281 0.238 0.2349 0.2868 0.2427 RANDOM 14.459
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] 0.638 -0.37 -0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.248 r_dihedral_angle_4_deg 18.313 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_1_deg 5.587 r_scangle_it 2.693 r_scbond_it 1.664 r_angle_refined_deg 1.333 r_mcangle_it 1.21 r_mcbond_it 0.673 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.248 r_dihedral_angle_4_deg 18.313 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_1_deg 5.587 r_scangle_it 2.693 r_scbond_it 1.664 r_angle_refined_deg 1.333 r_mcangle_it 1.21 r_mcbond_it 0.673 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing