8Q1F | pdb_00008q1f

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

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 10 mM bG16BP 28% PEG 4000 100 mM sodium acetate 100 mM tris

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.023	α = 90
b = 79.663	β = 97.614
c = 79.848	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		2023-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9801	Diamond	I03

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	1.01	39.83	80.3	0.038	0.016	0.999	26	6.3		166355			7.8

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	1.01	1.03			0.494	0.386	0.743	0.8	1.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.01	39.83	166313	8222	80.296	0.116	0.1152	0.11	0.1348	0.13	14.316

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]
-0.047		0.046	0.618		-0.564

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	28.835
r_dihedral_angle_6_deg	14.984
r_dihedral_angle_3_deg	12.209
r_dihedral_angle_1_deg	5.525
r_dihedral_angle_2_deg	4.599
r_angle_refined_deg	1.486
r_angle_other_deg	0.519
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.235
r_nbd_other	0.198
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.123
r_metal_ion_refined	0.106
r_xyhbond_nbd_refined	0.101
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.075
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3412
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	67

Software

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