2YBQ

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

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		PROTEIN WAS CRYSTALLIZED FROM 1.26 M AMMONIUM SULFATE, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.44	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.853	α = 90
b = 116.702	β = 90
c = 76.988	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	MARRESEARCH		2010-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	35	92.6	0.08	22.8	3.9		18362		2	34.4

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		0.45	4	4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2YBO	2	32.13	17443	919	100	0.22795	0.22626	0.25904	RANDOM	33.641

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]
-0.14			1.17		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.981
r_dihedral_angle_4_deg	20.273
r_dihedral_angle_3_deg	14.191
r_dihedral_angle_1_deg	5.24
r_scangle_it	2.721
r_scbond_it	1.606
r_angle_refined_deg	1.314
r_mcangle_it	1.025
r_mcbond_it	0.563
r_nbtor_refined	0.303
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.129
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	1817
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing