3FXK | pdb_00003fxk

Crystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Phosphate at 10 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, 10mM MnCl2, pH 5.2, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.76	α = 90
b = 90.76	β = 90
c = 105.711	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)	R Sym 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	2.1	27.832	98.8	0.065	0.065	10.18	9.6		29451

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.21	98.3		0.353	0.353	2.2	9.7	4240

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.1	15	29362	1486	98.55	0.198	0.196	0.2	0.234	0.23	RANDOM	27.384

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]
-0.1	-0.05		-0.1		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.588
r_dihedral_angle_4_deg	21.988
r_dihedral_angle_3_deg	15.927
r_dihedral_angle_1_deg	5.726
r_scangle_it	3.169
r_scbond_it	1.923
r_angle_refined_deg	1.272
r_mcangle_it	1.171
r_mcbond_it	0.683
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.588
r_dihedral_angle_4_deg	21.988
r_dihedral_angle_3_deg	15.927
r_dihedral_angle_1_deg	5.726
r_scangle_it	3.169
r_scbond_it	1.923
r_angle_refined_deg	1.272
r_mcangle_it	1.171
r_mcbond_it	0.683
r_nbtor_refined	0.299
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.16
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2828
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.