2PMI | pdb_00002pmi

Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway with Bound ATP-gamma-S

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PK9	PDB ENTRY 2PK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	283	9ul 12% PEG 10000, 10% glycerol, 0.05 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
4.74	74.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.592	α = 90
b = 146.592	β = 90
c = 212.848	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	200	CCD	ADSC QUANTUM 4	APS 19ID	2006-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0332	APS	19-ID

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	2.9	14.98	91.1	0.099	0.099	11	3.1	53704	53704		1	33.4

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	2.9	3	75.6		0.248	0.248	2.4	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PK9	2.9	14.98	53704	53533	2707	91.2	0.289	0.289	0.28	0.325	0.32	RANDOM	49.5

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]
0.43			0.43		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22
c_scangle_it	7.76
c_mcangle_it	6.07
c_scbond_it	5.27
c_mcbond_it	3.77
c_improper_angle_d	1.94
c_angle_deg	1.3
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8083
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	55

Software

Software
Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing