3CXK | pdb_00003cxk

1.7 A Crystal structure of methionine-R-sulfoxide reductase from Burkholderia pseudomallei: crystallization in a microfluidic crystal card.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CEZ	PDB entry 3CEZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROFLUIDIC MICROBATCH IN A CRYSTAL CARD	4.5	293	30% MPD, 0.1M Acetate, 25% PEG 1500, pH 4.5, MICROFLUIDIC MICROBATCH IN A CRYSTAL CARD, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.997	α = 88.41
b = 45.171	β = 83.73
c = 45.402	γ = 69.1

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	CUSTOM-MADE	Adjustable focusing mirrors	2008-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979315	APS	19-BM

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	1.7	50	95.3	0.068	8	3.6		32539

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	1.7	1.76	87.4		0.423		3.3	3023

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3CEZ	1.7	40	32478	1650	95.21	0.167	0.166	0.17	0.199	RANDOM	22.823

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]
0.43	-1.35	1.06		-0.27	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.666
r_dihedral_angle_4_deg	13.786
r_dihedral_angle_3_deg	11.73
r_dihedral_angle_1_deg	6.049
r_scangle_it	4.298
r_scbond_it	2.684
r_mcangle_it	1.781
r_angle_refined_deg	1.408
r_mcbond_it	1.012
r_angle_other_deg	0.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.666
r_dihedral_angle_4_deg	13.786
r_dihedral_angle_3_deg	11.73
r_dihedral_angle_1_deg	6.049
r_scangle_it	4.298
r_scbond_it	2.684
r_mcangle_it	1.781
r_angle_refined_deg	1.408
r_mcbond_it	1.012
r_angle_other_deg	0.933
r_mcbond_other	0.279
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.