2YBQ | pdb_00002ybq

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YBOPDB ENTRY 2YBO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5PROTEIN WAS CRYSTALLIZED FROM 1.26 M AMMONIUM SULFATE, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4446.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.853α = 90
b = 116.702β = 90
c = 76.988γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2010-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
123592.60.0822.83.918362234.4
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)
122.0599.90.4544

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2YBO232.13174439191000.227950.226260.240.259040.28RANDOM33.641
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]
-0.141.17-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.981
r_dihedral_angle_4_deg20.273
r_dihedral_angle_3_deg14.191
r_dihedral_angle_1_deg5.24
r_scangle_it2.721
r_scbond_it1.606
r_angle_refined_deg1.314
r_mcangle_it1.025
r_mcbond_it0.563
r_nbtor_refined0.303
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1817
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing