4Y72 | pdb_00004y72

Human CDK1/CyclinB1/CKS2 With Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HCK	1hck, 2b9r, 1jst
experimental model	PDB	2B9R	1hck, 2b9r, 1jst
experimental model	PDB	1JST	1hck, 2b9r, 1jst

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.7	277	Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.166	α = 90
b = 68.646	β = 90
c = 166.771	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97957	Diamond	I02

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	2.3	53	99.9	0.086	13.7	6.7	34085	34085

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)
1	2.3	2.38	99.9		0.778	2.4	6.4

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	1hck, 2b9r, 1jst	2.3	53	34010	1697	99.82	0.1895	0.1861	0.19	0.2519	0.2514	RANDOM	48.7092

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]
-0.41			-0.68		1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.587
r_dihedral_angle_4_deg	16.486
r_dihedral_angle_3_deg	16.044
r_dihedral_angle_1_deg	6.567
r_angle_other_deg	3.568
r_mcangle_it	2.273
r_angle_refined_deg	1.568
r_mcbond_it	1.279
r_mcbond_other	1.279
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_other	0.008
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5139
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement