3EZR | pdb_00003ezr

CDK-2 with indazole inhibitor 17 bound at its active site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	14% PEG 4K, 50mM Hepes pH 7.5, 50mM ammonium acetate, 10 mM DTT, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.763	α = 90
b = 72.081	β = 90
c = 72.392	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Blue Mirrors	2007-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	18.79				22762	22591

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	1.9	18.79	22591	1159	99.12	0.208	0.206	0.21	0.243	0.25	RANDOM	44.822

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]
-1.3			2.44		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.722
r_dihedral_angle_4_deg	15.182
r_dihedral_angle_3_deg	13.867
r_dihedral_angle_1_deg	5.618
r_scangle_it	2.196
r_scbond_it	1.407
r_angle_refined_deg	1.298
r_mcangle_it	1.268
r_angle_other_deg	0.821
r_mcbond_it	0.737
r_symmetry_vdw_refined	0.3
r_symmetry_vdw_other	0.279
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.2
r_nbtor_refined	0.196
r_nbd_other	0.186
r_xyhbond_nbd_refined	0.133
r_mcbond_other	0.113
r_nbtor_other	0.083
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2201
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	68

Software

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