3R8V | pdb_00003r8v

CDK2 in complex with inhibitor RC-1-135

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PW2	PDB ENTRY 1PW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	5 mg/mL CDK2 protein, 3 mM inhibitor, 15% v/v PEG3350, 50 mM HEPES/NaOH, 50 mM Na/K phosphate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.28	α = 90
b = 71.87	β = 90
c = 72.28	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	93	CCD	RIGAKU SATURN 944+	MIRRORS	2008-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.9	36.14	96.9	0.065	53.08	7.2	21860	21860		-3	15.6

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	1.9	1.97	94.8		0.25	13.27	7.3	2099

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 1PW2	1.9	36.14	21555	21555	1033	95.7	0.192	0.192	0.19	0.229	0.22	RANDOM	24.4

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]
-3.45			-2.89		6.34

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.7
c_scangle_it	2.73
c_mcangle_it	2.12
c_scbond_it	1.8
c_angle_deg	1.4
c_mcbond_it	1.3
c_improper_angle_d	0.89
c_bond_d	0.009
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	2366
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	21

Software

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