6I03

D10N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with tetrafluoroaluminate and beta-G6P to 1.02 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	291	24-34% PEG 4000 200 mM sodium acetate 50 mM TRIS, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.52	α = 90
b = 54.28	β = 90
c = 104.42	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-F		2015-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.02	37.52	97.6	0.045	0.054	0.021	0.999	16.1	6.5		106736

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	1.02	1.05	82.5		0.917	1.209	0.589	0.542	1.3	3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WF6	1.02	35.33	101274	5373	97.6	0.15265	0.15147	0.1747	RANDOM	16.192

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]
0.51			-0.97		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.317
r_sphericity_bonded	24.744
r_rigid_bond_restr	24.172
r_sphericity_free	19.127
r_dihedral_angle_4_deg	18.779
r_dihedral_angle_3_deg	11.849
r_dihedral_angle_1_deg	5.957
r_long_range_B_refined	2.631
r_long_range_B_other	2.451
r_scangle_other	2.392
r_scbond_other	2.138
r_scbond_it	2.137
r_mcangle_other	2.065
r_mcangle_it	1.974
r_mcbond_it	1.912
r_mcbond_other	1.856
r_angle_other_deg	1.52
r_angle_refined_deg	1.507
r_chiral_restr	0.069
r_gen_planes_refined	0.009
r_bond_refined_d	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1692
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing