3NIW | pdb_00003niw

Crystal structure of a haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	294	100mM sodium acetate pH 4.6, 30% PEG 4K, 200mM ammonium acetate, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.773	α = 90
b = 72.716	β = 90
c = 82.4	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315		2010-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97890	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	30	99.75	0.085	0.085	13.3	14.1	21353	21300			23

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)
	1.9	1.93	100		0.353		14.5	1018

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.9	20	21346	21229	1084	99.78	0.1783	0.1769	0.18	0.206	0.21	RANDOM	28.3668

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]
1.66			-0.41		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.829
r_dihedral_angle_4_deg	22.61
r_dihedral_angle_3_deg	13.723
r_dihedral_angle_1_deg	5.872
r_scangle_it	4.437
r_scbond_it	2.544
r_mcangle_it	1.569
r_angle_refined_deg	1.446
r_angle_other_deg	0.948
r_mcbond_it	0.854

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.829
r_dihedral_angle_4_deg	22.61
r_dihedral_angle_3_deg	13.723
r_dihedral_angle_1_deg	5.872
r_scangle_it	4.437
r_scbond_it	2.544
r_mcangle_it	1.569
r_angle_refined_deg	1.446
r_angle_other_deg	0.948
r_mcbond_it	0.854
r_mcbond_other	0.221
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2077
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	7

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building
Coot	model building

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.