3FXO

Crystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Phosphate at 1 mM of Mn2+

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	277	50mM potassium phosphate, 12%(w/v) PEG8000, 15%(v/v) glycerol, 2mM DTT, 1mM MnCl2, pH 5.2, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.115	α = 90
b = 91.115	β = 90
c = 106.577	γ = 120

Symmetry
Space Group	P 31 2 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	IMAGE PLATE	RIGAKU RAXIS IV++		2008-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.5	29.82	99.5	0.137		5.42		18059

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)
	2.5	2.59	100		0.369	2	5.43	1791

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		THROUGHOUT	2.5	15	17984	912	99.56	0.193	0.19	0.251	RANDOM	25.21

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]
-0.15	-0.07		-0.15		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.715
r_dihedral_angle_4_deg	21.47
r_dihedral_angle_3_deg	16.55
r_dihedral_angle_1_deg	5.417
r_scangle_it	1.836
r_angle_refined_deg	1.131
r_scbond_it	1.05
r_mcangle_it	0.784
r_mcbond_it	0.428
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.715
r_dihedral_angle_4_deg	21.47
r_dihedral_angle_3_deg	16.55
r_dihedral_angle_1_deg	5.417
r_scangle_it	1.836
r_angle_refined_deg	1.131
r_scbond_it	1.05
r_mcangle_it	0.784
r_mcbond_it	0.428
r_nbtor_refined	0.299
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.098
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2821
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	12

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.