5OK0

Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WF5

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.81	α = 90
b = 54.94	β = 90
c = 103.34	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 PILATUS3 6M		2016-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	48.51	100	0.339	0.148	0.98	5.3	6.2		11990

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	100		1.683	0.721	0.391	1.2	6.4

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	2WF5	2.15	48.51	11376	571	99.88	0.2235	0.2201	0.29234	RANDOM	31.793

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]
-1.75			-0.87		2.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.342
r_dihedral_angle_3_deg	15.83
r_dihedral_angle_4_deg	11.012
r_dihedral_angle_1_deg	6.524
r_long_range_B_refined	4.902
r_long_range_B_other	4.901
r_scangle_other	3.546
r_mcangle_other	2.782
r_mcangle_it	2.781
r_scbond_it	2.186
r_scbond_other	2.184
r_mcbond_it	1.774
r_mcbond_other	1.739
r_angle_refined_deg	1.495
r_angle_other_deg	0.997
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1680
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
xia2	data scaling