3C13 | pdb_00003c13

Low pH-value crystal structure of emodin in complex with the catalytic subunit of protein kinase CK2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BQC	PDB entry 3BQC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	Protein stock solution: 10mg/ml protein in 500mM NaCl, 25mM Tris/HCl, pH 8.5 Emodin stock solution: 10mM in water Protein/emodin mixture: equal volumes of protein and emodin stock solutions were mixed and equillibrated for 30 min prior to crystallization Reservoir: 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6 Crystallization drop: 2 microliters protein/emodin mixture plus 1 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.73	α = 90
b = 45.68	β = 111.8
c = 63.24	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 225 mm CCD		2007-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9537	EMBL/DESY, HAMBURG	X12

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	1.95	19.7	99.9	0.112	0.112	13.9	4.5	22799	22776			25.1

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	1.95	2.02	100		0.626	0.626	2	4.5	2247

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 (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 entry 3BQC	1.95	19.7	22776	21615	1161	99.67	0.1877	0.1877	0.18522	0.2	0.23346	0.25	RANDOM	24.78

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]
-3.39		0.37	3.52		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.282
r_dihedral_angle_4_deg	18.86
r_dihedral_angle_3_deg	14.57
r_dihedral_angle_1_deg	5.963
r_scangle_it	4.748
r_mcangle_it	4.315
r_mcbond_it	3.833
r_scbond_it	3.674
r_angle_refined_deg	1.397
r_mcbond_other	1.31
r_angle_other_deg	0.918
r_symmetry_vdw_other	0.264
r_nbd_refined	0.215
r_nbd_other	0.196
r_symmetry_hbond_refined	0.192
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.179
r_symmetry_vdw_refined	0.136
r_nbtor_other	0.089
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2773
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling