3D64 | pdb_00003d64

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.25	289	21.5 mg/ml Protein, 20% PEG 3350, 200mM Na acetate, 5% Glycerol, 25mM Hepes, 500mM NaCl, 0.025M Na Azide, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.8	74.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.363	α = 90
b = 186.363	β = 90
c = 104.403	γ = 120

Symmetry
Space Group	P 32 2 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	MARMOSAIC 300 mm CCD		2008-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03317	APS	23-ID-D

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	2.3	50	100	0.125	7.7	6.8		92618

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	2.3	2.38	99.9		0.649		6	9144

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	50	92580	4633	99.97	0.172	0.171	0.18	0.202	0.21	RANDOM	21.578

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]
0.95	0.48		0.95		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.361
r_dihedral_angle_4_deg	17.417
r_dihedral_angle_3_deg	14.661
r_dihedral_angle_1_deg	6.176
r_scangle_it	3.181
r_scbond_it	1.922
r_angle_refined_deg	1.246
r_mcangle_it	1.163
r_angle_other_deg	1.044
r_mcbond_it	0.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.361
r_dihedral_angle_4_deg	17.417
r_dihedral_angle_3_deg	14.661
r_dihedral_angle_1_deg	6.176
r_scangle_it	3.181
r_scbond_it	1.922
r_angle_refined_deg	1.246
r_mcangle_it	1.163
r_angle_other_deg	1.044
r_mcbond_it	0.578
r_mcbond_other	0.111
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7180
Nucleic Acid Atoms
Solvent Atoms	708
Heterogen Atoms	88

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

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.