7P5O

Crystal structure of Aspergillus fumigatus phosphoglucomutase in complex with the reaction intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EPC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	90 mM sodium fluoride, 90 mM sodium bromide, 90 mM sodium iodide, 100 mM Tris-bicine pH 8.5, 20% v/v polyethylene glycol 550 MME, 10 % w/v polyethylene glycol 20000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.57	α = 90
b = 209.61	β = 90
c = 61.2	γ = 90

Symmetry
Space Group	P 21 21 2

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 EIGER X 4M		2016-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967700	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.48	89.2	98.4	0.994	11.2	4.2		44960

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.48	2.53			0.795

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	5EPC	2.48	89.2	42710	2250	98.39	0.2041	0.2011	0.2584	RANDOM	37.597

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]
-2.75			0.24		2.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.691
r_dihedral_angle_4_deg	24.033
r_dihedral_angle_3_deg	18.859
r_dihedral_angle_1_deg	7.523
r_angle_refined_deg	1.629
r_angle_other_deg	1.272
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.691
r_dihedral_angle_4_deg	24.033
r_dihedral_angle_3_deg	18.859
r_dihedral_angle_1_deg	7.523
r_angle_refined_deg	1.629
r_angle_other_deg	1.272
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8545
Nucleic Acid Atoms
Solvent Atoms	510
Heterogen Atoms	42

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling

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 R01GM133198.