3RK5 | pdb_00003rk5

CDK2 in complex with inhibitor RC-2-72

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
2	38.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.35	α = 90
b = 71.83	β = 90
c = 72.42	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	2008-11-23	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	2	20	99.7	0.064	18.95	6.16	19336	19336		-3	15

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	2.05	99.6		0.341	6.15	6.12	1361

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	2	18.76	19336	19336	1103	99.7	0.206	0.206	0.2	0.238	0.23	RANDOM	33.6

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]
-1.19			-6.03		7.22

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.5
c_scangle_it	2.66
c_mcangle_it	2.49
c_scbond_it	1.74
c_mcbond_it	1.45
c_angle_deg	1.4
c_improper_angle_d	0.88
c_bond_d	0.01
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	134
Heterogen Atoms	24

Software

Software
Software Name	Purpose
StructureStudio	data collection
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing