8H4R | pdb_00008h4r

The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.6M MgSO4, 0.1M MES pH 6.60

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.027	α = 90
b = 155.027	β = 90
c = 76.788	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2022-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95372	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.75	44.75	99.1	0.976	7.3	4		27244

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.9	99.1		0.577	2.1	4.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.75	42.371	27237	1385	98.846	0.164	0.1614	0.17	0.2234	0.23	35.299

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]
0.571	0.285		0.571		-1.851

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.849
r_lrange_other	14.24
r_lrange_it	14.227
r_dihedral_angle_6_deg	12.64
r_scangle_it	10.18
r_scangle_other	10.179
r_mcangle_it	7.939
r_mcangle_other	7.939
r_dihedral_angle_2_deg	7.838
r_scbond_it	6.865
r_scbond_other	6.864
r_dihedral_angle_1_deg	5.778
r_mcbond_it	5.273
r_mcbond_other	5.273
r_angle_refined_deg	1.129
r_angle_other_deg	0.361
r_nbd_refined	0.194
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.163
r_symmetry_nbd_refined	0.162
r_nbd_other	0.156
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.05
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4577
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing