8Q1E

D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WF9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	290	0.6 mM bPGM-D10N,P146A 50 mM MgCl2 50 mM F16BP 32 % PEG 4000 100 mM sodium acetate 100 mM tris

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.12	α = 90
b = 83.757	β = 110.661
c = 38.89	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	100	PIXEL	DECTRIS EIGER2 XE 16M		2023-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9227	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	1.23	83.76	100	0.074	0.031	0.999	12.3	6.8		55719			14.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.25	98		0.953	0.315	0.4	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.23	41.913	55684	2670	99.898	0.154	0.1516	0.1942	27.565

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]
-0.606		0.505	0.069		0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	20.112
r_dihedral_angle_6_deg	14.827
r_dihedral_angle_3_deg	13.922
r_dihedral_angle_1_deg	5.271
r_dihedral_angle_2_deg	4.84
r_angle_refined_deg	1.185
r_angle_other_deg	0.42
r_nbd_refined	0.228
r_nbd_other	0.226
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.174
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.101
r_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.058
r_metal_ion_refined	0.028
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1706
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	27

Software

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