Experiment: 6YDL

Substrate-free beta-phosphoglucomutase from Lactococcus lactis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WHE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	PEG 4000, sodium acetate (200 mM), tris (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.6 mM)

Crystal Properties
Matthews coefficient	Solvent content
9.76	87.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.28	α = 90
b = 54.07	β = 90
c = 81.85	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	PIXEL	DECTRIS PILATUS 6M		2016-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.52	44.65	99.3	0.044	0.051	0.019	1	18.8	7.2		36815			21.233

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.56	99.3		1.19	1.428	0.561	0.5	1.3	6.3

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	2WHE	1.52	44.65	34940	1818	99.06	0.18415	0.18252	0.1943	0.21606	0.2209	Random selection	27.046

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]
0.96			-0.08		-0.88

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1689
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction