6H91 | pdb_00006h91

Phosphorylated beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 2.4 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	24-34% PEG 4000, 200 mM sodium acetate, 50 mM TRIS pH 7.5, The crystal was cryoprotected in its original mother liquor plus an additional 25% ethylene glycol and 30mM acetylphosphate.

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.33	α = 90
b = 117.23	β = 97.75
c = 52.93	γ = 90

Symmetry
Space Group	P 1 21 1

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		2015-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97779	Diamond	I03

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	2.38	58.62	99	0.12	0.165	0.084	0.987	6.7	3.7		18430

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	2.38	2.44	98.9		0.597	0.813	0.438	0.526		3.3

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	2.38	58.62	17460	945	99.01	0.22299	0.2188	0.22	0.29875	0.3	RANDOM	40.3

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]
0.47		0.01	-0.24		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.525
r_dihedral_angle_4_deg	17.516
r_dihedral_angle_3_deg	16.438
r_dihedral_angle_1_deg	6.588
r_long_range_B_other	5.74
r_long_range_B_refined	5.735
r_scangle_other	3.78
r_mcangle_it	3.38
r_mcangle_other	3.379
r_scbond_it	2.345
r_scbond_other	2.345
r_mcbond_it	2.183
r_mcbond_other	2.182
r_angle_refined_deg	1.539
r_angle_other_deg	0.967
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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	3368
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	22

Software

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