5MUF

Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal WDPNWD motif

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	18% PEG 3350 and 0.1 M MES, pH 5.7

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.215	α = 90
b = 141.403	β = 90
c = 183.12	γ = 90

Symmetry
Space Group	I 2 2 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 PILATUS3 6M		2011-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97630	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	3.1	41.03	94.3	0.271	0.101	6.8	7		18243			55.3

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	3.1	3.27	96.2		0.993	0.373	2	6.9

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	3MXO	3.1	41.03	17300	933	92.4	0.22793	0.22648	0.25553	RANDOM	50.597

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]
0.49			1.02		-1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.083
r_dihedral_angle_3_deg	15.347
r_dihedral_angle_4_deg	13.027
r_dihedral_angle_1_deg	6.308
r_long_range_B_refined	2.385
r_long_range_B_other	2.385
r_mcangle_it	1.156
r_mcangle_other	1.156
r_angle_refined_deg	1.104
r_scangle_other	0.881
r_angle_other_deg	0.779
r_mcbond_it	0.623
r_mcbond_other	0.623
r_scbond_it	0.466
r_scbond_other	0.462
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5062
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing