5EQA

Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) with intermolecular cross-link between Lys158 and Cys245

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	30% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 10 mM magnesium acetate. Crystals were incubated overnight over the reservoir supplemented with 100 mM formaldehyde to complete cross-linking between Lys158 and Cys245 and vitrified in Paraton-N

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.24	α = 90
b = 89.39	β = 96.93
c = 92.24	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	CCD	RAYONIX MX300-HS		2015-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.7999	APS	22-ID

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	1.32	40	99.9	0.065	12	5.1		234185

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.35	99.9		0.71	2	4.2

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	FREE R-VALUE	1.32	36.2	231842	2342	99.87	0.125	0.124	0.165	RANDOM	23.274

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]
0.74		-0.29	-0.02		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.946
r_sphericity_free	36.321
r_sphericity_bonded	15.491
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	13.36
r_dihedral_angle_1_deg	6.178
r_long_range_B_refined	5.687
r_long_range_B_other	4.943
r_scangle_other	4.505
r_rigid_bond_restr	4.223
r_scbond_it	3.807
r_scbond_other	3.807
r_mcangle_other	3.059
r_mcangle_it	3.058
r_mcbond_it	2.564
r_mcbond_other	2.559
r_angle_refined_deg	2
r_angle_other_deg	1.213
r_chiral_restr	0.15
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.003
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	7891
Nucleic Acid Atoms
Solvent Atoms	1071
Heterogen Atoms	9

Software

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