5O6R | pdb_00005o6r

Structure of beta-phosphoglucomutase D10N mutant in complex with glucose-1-phosphate and aluminium tetrafluoride

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	19-21 % PEG 3350 and 50 mM Mg acetate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.3	α = 90
b = 54.9	β = 90
c = 107.56	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	CCD	ADSC QUANTUM 210r		2008-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.36	53.78	93.6	0.027	24.5	3		43148	3		11.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.36	1.44	91.3		0.11	0.077	7.4	2.8

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	1o08	1.36	20	40948	2183	91.93	0.11652	0.11473	0.13	0.14898	0.16	RANDOM	13.314

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]
0.08			-0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.576
r_sphericity_free	22.969
r_dihedral_angle_4_deg	16.782
r_dihedral_angle_3_deg	11.015
r_sphericity_bonded	7.126
r_dihedral_angle_1_deg	5.474
r_long_range_B_refined	2.693
r_long_range_B_other	2.692
r_rigid_bond_restr	2.06
r_scangle_other	1.885
r_angle_refined_deg	1.741
r_scbond_other	1.581
r_scbond_it	1.578
r_mcangle_other	1.142
r_mcangle_it	1.134
r_angle_other_deg	1.012
r_mcbond_it	0.889
r_mcbond_other	0.835
r_chiral_restr	0.287
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1680
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing