6YDM

beta-phosphoglucomutase from Lactococcus lactis with citrate, tris and acetate bound

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	PEG 4000, sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), trisodium citrate (50 mM), beta-phosphoglucomutase (0.6 mM)

Crystal Properties
Matthews coefficient	Solvent content
9.86	87.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.13	α = 90
b = 76.64	β = 90
c = 117.26	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 PILATUS3 6M		2018-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97179	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	117.3	97.5	0.098	0.033	0.999	13.7	8.6		27995			24.2

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	2.1	2.16	90.1		0.536	0.574	0.198	0.899	3.7	7.6

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WHE	2.1	46.61	27947	1349	97.332	0.233	0.2299	0.2897	RANDOM	31.766

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]
-0.242			2.269		-2.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.019
r_dihedral_angle_3_deg	15.722
r_dihedral_angle_4_deg	14.703
r_dihedral_angle_1_deg	6.628
r_lrange_other	5.49
r_lrange_it	5.488
r_scangle_it	4.09
r_scangle_other	4.089
r_scbond_it	2.83
r_scbond_other	2.83
r_mcangle_it	2.795
r_mcangle_other	2.795
r_mcbond_it	2.148
r_mcbond_other	2.064
r_angle_refined_deg	1.482
r_angle_other_deg	1.302
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.159
r_nbd_other	0.145
r_ncsr_local_group_1	0.079
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
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	3374
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	40

Software

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