2BCD | pdb_00002bcd

X-ray crystal structure of Protein Phosphatase-1 with the marine toxin motuporin bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JK7	PDB ID 1JK7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	273	2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%), beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.955	α = 90
b = 100.955	β = 90
c = 63.485	γ = 90

Symmetry
Space Group	P 42 21 2

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	ADSC QUANTUM 4	mirrors	2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

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	45.13	99.9	0.065	0.065	7.1	3.7		19722		3

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)
1	2	2.21	100	100	0.293	0.293	2.5	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 1JK7	2.1	31.75	3	19682	1008	99.92	0.223	0.223	0.221	0.22	0.264	0.27	RANDOM	26.439

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.609
r_dihedral_angle_4_deg	15.697
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	6.782
r_scangle_it	2.943
r_scbond_it	2.116
r_angle_refined_deg	1.838
r_mcangle_it	1.486
r_mcbond_it	0.926
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.609
r_dihedral_angle_4_deg	15.697
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	6.782
r_scangle_it	2.943
r_scbond_it	2.116
r_angle_refined_deg	1.838
r_mcangle_it	1.486
r_mcbond_it	0.926
r_nbtor_refined	0.3
r_xyhbond_nbd_refined	0.169
r_symmetry_vdw_refined	0.169
r_nbd_refined	0.155
r_chiral_restr	0.117
r_symmetry_hbond_refined	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2405
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

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.