3F5X | pdb_00003f5x

CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	14% PEG 4000, 50mM Hepes pH 7.5, 50mM ammonium acetate, 10 mM DTT, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.051	α = 90
b = 184.051	β = 90
c = 214.848	γ = 120

Symmetry
Space Group	P 62 2 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	IMAGE PLATE	RIGAKU RAXIS IV		2006-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	2.3	20	99.5	0.092				94535

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.4	20	83276	4169	99.2	0.266	0.266	0.27	0.283	0.29	RANDOM	53.98

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]
0.98	0.49		0.98		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.217
r_dihedral_angle_4_deg	17.446
r_dihedral_angle_3_deg	16.031
r_dihedral_angle_1_deg	6.526
r_scangle_it	1.484
r_angle_other_deg	1.231
r_angle_refined_deg	1.155
r_scbond_it	0.933
r_mcangle_it	0.902
r_mcbond_it	0.518
r_nbd_refined	0.204
r_symmetry_vdw_other	0.197
r_symmetry_hbond_refined	0.188
r_nbd_other	0.182
r_nbtor_refined	0.179
r_chiral_restr	0.174
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.113
r_nbtor_other	0.088
r_mcbond_other	0.085
r_bond_refined_d	0.008
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8920
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction