Experiment: 9SQB

D-stereospecific hydrolase I from Bacillus thuringiensis Berliner 1915 in complex with benzoyl-D-arginine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	0.1 M imidazole, 0.1 M MES pH 6.5, 30 mM MgCl2, 30 mM CaCl2, 12.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) polyethylene glycol 3350 (Morpheus screen, Molecular Dimensions). Protein concentration: 120 uM in 0.1 M phosphate buffer (pH 8.0), 0.1 M NaCl. Hanging drop vapor diffusion mixing 1:1 protein and precipitant solution. Crystals were soaked for 30 min in crystallisation buffer supplemented with 0.5 M Bz-D-Arg-OMe.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.279	α = 90
b = 95.581	β = 105.53
c = 68.931	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	101.15	CCD	MARMOSAIC 225 mm CCD	Focussing mirror	2013-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.66	20	99.8	0.056	17.8	3.8		84136

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	1.66	1.75	99.8		0.801	2	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.66	19.662	1.35	84136	4197	99.84	0.1586	0.1566	0.1559	0.1966	0.1958

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.821
f_angle_d	1.028
f_chiral_restr	0.071
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5143
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	57

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction