3Q9Z | pdb_00003q9z

Crystal structure of human CK2 alpha in complex with Quinalizarin at pH 6.5

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M Mes pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.956	α = 90
b = 127.956	β = 90
c = 125.739	γ = 90

Symmetry
Space Group	P 43 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 315r		2007-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976234	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	89.68	95.6	0.08	7.2	2.2	50758	50758

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	85		0.636	0.636	0.815	0.499	0.5	2.1	6521

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PVR	2.2	57.22	50723	2564	94.83	0.2153	0.2126	0.2071	0.2666	0.258	RANDOM	44.8147

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]
1			1		-2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.129
r_dihedral_angle_4_deg	22.583
r_dihedral_angle_3_deg	17.896
r_dihedral_angle_1_deg	6.455
r_scangle_it	4.625
r_scbond_it	2.907
r_angle_refined_deg	1.867
r_mcangle_it	1.727
r_mcbond_it	0.942
r_chiral_restr	0.131
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5608
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	79

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
MOSFLM	data reduction
PHASER	phasing