3CEZ

Crystal structure of methionine-R-sulfoxide reductase from Burkholderia pseudomallei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L1D	PDB entry 1L1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	15% Ethanol, 100 mM MES pH 6.0, 200 mM Zn(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.093	α = 87.35
b = 45.782	β = 83.22
c = 45.812	γ = 69.36

Symmetry
Space Group	P 1

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 SATURN 944	Mirrors	2008-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.1	31.42	94.6	0.11	9.21	3.9		17575		2	28.7

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	2.1	2.18	85.1		0.34	2.8	3.8	1583

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 (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 1L1D	2.1	31.42	16682	892	94.41	0.17896	0.17612	0.18	0.23367	0.24	RANDOM	19.61

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]
0.7	-0.92	-0.13	0.39	-0.01	-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.055
r_dihedral_angle_4_deg	11.825
r_dihedral_angle_3_deg	11.439
r_dihedral_angle_1_deg	6.52
r_scangle_it	2.468
r_scbond_it	1.763
r_angle_refined_deg	1.248
r_mcangle_it	1.225
r_angle_other_deg	0.911
r_mcbond_it	0.816
r_symmetry_vdw_other	0.263
r_symmetry_vdw_refined	0.207
r_nbd_other	0.2
r_nbd_refined	0.192
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.139
r_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	2038
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling