Experiment: 2GDV

Sucrose phosphorylase from BIFIDOBACTERIUM ADOLESCENTIS reacted with sucrose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	PEG 4000, SODIUM ACETATE, TRIS, bicine, sucrose, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.74	α = 90
b = 103.07	β = 90
c = 150.69	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	120	IMAGE PLATE	MAR scanner 345 mm plate		2003-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.841	EMBL/DESY, HAMBURG	BW7B

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	20	99.6	0.082	21.5		80388	80388			14.9

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)
	2	2.07	96.9		0.433	2.6

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1R7A	2	19.89	79924	4028	99.6	0.2	0.198	0.2043	0.237	0.2415	RANDOM	27.2

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]
-3.94			8.28		-4.34

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_scangle_it	2.92
c_angle_deg	2.3
c_scbond_it	1.98
c_mcangle_it	1.95
c_improper_angle_d	1.51
c_mcbond_it	1.26
c_bond_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7930
Nucleic Acid Atoms
Solvent Atoms	1006
Heterogen Atoms	23

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
CNS	phasing