6H8W | pdb_00006h8w

Beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with aluminium tetrafluoride to 1.9 A.

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	7.2	291	Crystals initially grown as open beta-phosphoglucomutase crystals, using 24-32% PEG 4000, 200mM sodium acetate, 50 mM TRIS buffer pH 7.5. Crystals were cryoprotected in their original mother liquor with the addition of 25% ethylene glycol, 5 mM aluminium chloride and 20 mM sodium fluoride.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.44	α = 90
b = 53.71	β = 90
c = 80.88	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		2015-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

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	1.98	40.44	99.8	0.116	0.156	0.075	0.992	9.5	4.3	71414	19779

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	1.98	2.03	99.9		0.738	0.969	0.459	0.576		4.3

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	2WHE	1.98	40.44	15929	807	99.79	0.20666	0.20457	0.21	0.24806	0.25	RANDOM	24.376

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]
1.12			-1.08		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.341
r_dihedral_angle_4_deg	21.855
r_dihedral_angle_3_deg	14.096
r_dihedral_angle_1_deg	5.848
r_long_range_B_refined	4.49
r_long_range_B_other	4.45
r_scangle_other	3.174
r_mcangle_it	2.475
r_mcangle_other	2.474
r_scbond_other	2.045
r_scbond_it	2.044
r_mcbond_it	1.665
r_mcbond_other	1.665
r_angle_refined_deg	1.483
r_angle_other_deg	0.97
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1689
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
MOLREP	phasing
xia2	data reduction