2YBO

The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S4DPDB ENTRY 1S4D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18PROTEIN WAS CRYSTALLIZED FROM 24% PEG 6000, 0.1 M TRIS PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2946.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.9α = 90
b = 115.1β = 90
c = 76.8γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDMIRRORS2009-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1246.3199.80.0420.194.419360235.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.90.592.584.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S4D226.91521829491598.2810.2380.23490.2868RANDOM14.459
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.248
r_dihedral_angle_4_deg18.313
r_dihedral_angle_3_deg14.532
r_dihedral_angle_1_deg5.587
r_scangle_it2.693
r_scbond_it1.664
r_angle_refined_deg1.333
r_mcangle_it1.21
r_mcbond_it0.673
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.248
r_dihedral_angle_4_deg18.313
r_dihedral_angle_3_deg14.532
r_dihedral_angle_1_deg5.587
r_scangle_it2.693
r_scbond_it1.664
r_angle_refined_deg1.333
r_mcangle_it1.21
r_mcbond_it0.673
r_nbtor_refined0.31
r_symmetry_hbond_refined0.226
r_nbd_refined0.211
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.16
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms1858
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing