7XQK | pdb_00007xqk

The Crystal Structure of CDK3 and CyclinE1 Complex from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EOJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.6M MgSO4, 0.1M MES pH6.5

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.154	α = 90
b = 154.154	β = 90
c = 76.675	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 PILATUS3 6M		2022-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18078	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.25	44.5	100	0.139	0.998	15.9	10.2		49467

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.32			0.973	0.797	2.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4EOJ	2.25	44.5	49447	2457	99.97	0.162	0.1599	0.17	0.2024	0.21	38.105

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]
0.355	0.178		0.355		-1.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.76
r_dihedral_angle_4_deg	18.368
r_dihedral_angle_3_deg	14.056
r_lrange_it	9.487
r_lrange_other	9.477
r_scangle_it	6.411
r_scangle_other	6.41
r_dihedral_angle_1_deg	6.096
r_mcangle_it	5.064
r_mcangle_other	5.063
r_scbond_it	4.15
r_scbond_other	4.149
r_mcbond_it	3.302
r_mcbond_other	3.302
r_angle_refined_deg	1.494
r_angle_other_deg	1.307
r_symmetry_nbd_refined	0.238
r_nbd_other	0.236
r_nbd_refined	0.208
r_symmetry_nbd_other	0.175
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_other	0.107
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4580
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	85

Software

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