3FXM | pdb_00003fxm

Crystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Citrate 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 trisodium citrate, 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
2.93	57.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.069	α = 90
b = 91.069	β = 90
c = 106.508	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	14.97	97.5	0.153		7.06		17595

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	97.9		0.365	2	7.34	1733

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	2.5	14.97	17593	895	97.53	0.186	0.183	0.18	0.251	0.25	RANDOM	23.52

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]
-0.31	-0.16		-0.31		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.371
r_dihedral_angle_4_deg	21.757
r_dihedral_angle_3_deg	18.691
r_dihedral_angle_1_deg	5.973
r_scangle_it	2.617
r_scbond_it	1.518
r_angle_refined_deg	1.431
r_mcangle_it	0.982
r_mcbond_it	0.541
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.371
r_dihedral_angle_4_deg	21.757
r_dihedral_angle_3_deg	18.691
r_dihedral_angle_1_deg	5.973
r_scangle_it	2.617
r_scbond_it	1.518
r_angle_refined_deg	1.431
r_mcangle_it	0.982
r_mcbond_it	0.541
r_nbtor_refined	0.304
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2828
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	20

Software

Software
Software Name	Purpose
d*TREK	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.