3I76 | pdb_00003i76

The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ED5	PDB entry 3ED5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	294	100mM Tris HCl pH 8.5, 30% PEG 4K, 200mM magnesium chloride, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.685	α = 90
b = 67.964	β = 90
c = 271.404	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	MARMOSAIC 225 mm CCD		2009-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2	50	91.6	0.097	0.097	33.1	6.7	55918	51221			20.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	87.7		0.397	0.397	8.9	6.8	2392

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3ED5	2	20	55855	51018	2573	91.34	0.177	0.175	0.18	0.219	0.22	RANDOM	23.739

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]
-0.05			-1.39		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.352
r_dihedral_angle_4_deg	22.491
r_dihedral_angle_3_deg	15.072
r_dihedral_angle_1_deg	5.811
r_scangle_it	4.282
r_scbond_it	2.73
r_mcangle_it	1.707
r_angle_refined_deg	1.484
r_mcbond_it	0.94
r_angle_other_deg	0.929

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.352
r_dihedral_angle_4_deg	22.491
r_dihedral_angle_3_deg	15.072
r_dihedral_angle_1_deg	5.811
r_scangle_it	4.282
r_scbond_it	2.73
r_mcangle_it	1.707
r_angle_refined_deg	1.484
r_mcbond_it	0.94
r_angle_other_deg	0.929
r_mcbond_other	0.254
r_chiral_restr	0.093
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5569
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	14

Software

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

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.