2C6M | pdb_00002c6m

Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B39	PDB ENTRY 1B39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2		PEG3350, HEPES PH7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, pH 7.20

Crystal Properties
Matthews coefficient	Solvent content
2.1	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.662	α = 90
b = 71.702	β = 90
c = 72.384	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 MSC	MIRRORS	2003-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	30	95.2	0.04	15.1	2.3		21538

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	72.9		0.22	2.9	3.07

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	PDB ENTRY 1B39	1.9	15	19712	1791	95.2	0.201	0.195	0.21	0.27	0.27	RANDOM	36.2

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]
0.2			-1.09		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.933
r_scangle_it	3.992
r_scbond_it	2.628
r_mcangle_it	1.726
r_angle_refined_deg	1.564
r_mcbond_it	0.999
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2321
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing