6YDJ | pdb_00006ydj

P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with glucose 6-phosphate and trifluoromagnesate

X-RAY DIFFRACTION

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	7.5	290	PEG 4000 (32% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (13 mM), magnesium chloride (5 mM), EDTA (200 uM), sodium azide (500 uM), sodium fluoride (15 mM), glucose 6-phosphate (10 mM), beta-phosphoglucomutase (0.4 mM)

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.08	α = 90
b = 54.25	β = 90
c = 104.32	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		2018-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.04	54.25	99.9	0.067	0.073	0.028	0.999	12.4	6.7		101730			7.445

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	1.04	1.06	99.3		1.138	1.295	0.609	0.544	1.1	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WF5	1.04	52.21	96597	5041	99.81	0.1506	0.1497	0.16	0.1685	0.17	RANDOM	12.63

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]
-0.01			-0.36		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.791
r_dihedral_angle_4_deg	24.108
r_sphericity_free	22.635
r_dihedral_angle_3_deg	11.449
r_sphericity_bonded	6.597
r_dihedral_angle_1_deg	5.25
r_rigid_bond_restr	2.057
r_angle_refined_deg	1.473
r_angle_other_deg	0.908
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.791
r_dihedral_angle_4_deg	24.108
r_sphericity_free	22.635
r_dihedral_angle_3_deg	11.449
r_sphericity_bonded	6.597
r_dihedral_angle_1_deg	5.25
r_rigid_bond_restr	2.057
r_angle_refined_deg	1.473
r_angle_other_deg	0.908
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1678
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	31

Software

Software
Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.