8Q1D | pdb_00008q1d

D10N 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 5 mM MgCl2 50 mM fructose 1,6-bisphosphate 38 % PEG 4000 200 mM sodium acetate 100 mM tris

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.888	α = 90
b = 71.382	β = 90
c = 83.909	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 EIGER2 XE 16M		2020-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	1.75	54.429	100	0.151	0.043	0.998	10.5	13.1		20093			18.7

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	1.75	1.78	99.2		1.33	0.379	0.829	1.1	13

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	1.75	54.429	20040	965	99.915	0.165	0.161	0.17	0.252	0.26	28.344

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]
-2.477			3.688		-1.211

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.23
r_dihedral_angle_3_deg	13.539
r_dihedral_angle_1_deg	6.08
r_dihedral_angle_2_deg	4.331
r_angle_refined_deg	1.567
r_angle_other_deg	0.512
r_symmetry_nbd_refined	0.286
r_nbd_other	0.27
r_symmetry_xyhbond_nbd_refined	0.244
r_nbd_refined	0.222
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1708
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	33

Software

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