5MXM

The X-ray structure of human M190I phosphoglycerate kinase 1 mutant

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG MME 30% w/v, Bis Tris 0.1 M pH=7

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.363	α = 90
b = 91.104	β = 90
c = 109.01	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	RAYONIX MX-225		2016-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.3	0.894	BESSY	14.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	69.91	99.7	13.15	5.99		24685

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.05	69.91	23510	1190	99.73	0.17861	0.17623	0.22554	RANDOM	22.582

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]
-0.32			1.8		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.478
r_dihedral_angle_4_deg	20.027
r_dihedral_angle_3_deg	15.28
r_long_range_B_refined	9.278
r_long_range_B_other	9.277
r_dihedral_angle_1_deg	6.723
r_scangle_other	3.711
r_mcangle_it	2.506
r_mcangle_other	2.506
r_scbond_it	2.38
r_scbond_other	2.379
r_angle_refined_deg	1.953
r_mcbond_other	1.663
r_mcbond_it	1.662
r_angle_other_deg	1.047
r_chiral_restr	0.127
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
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	3110
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing