8K5R

CDK9/cyclin T1 in complex with KB-0742

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BLH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2M K3 citrate, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
4	69.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.502	α = 90
b = 171.502	β = 90
c = 96.122	γ = 120

Symmetry
Space Group	H 3

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 16M		2021-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.99999	SPring-8	BL41XU

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	3.75	85.751	99.7	0.062	11.6	4.7		10792

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	3.75	4.19			0.683

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.751	85.751	10789	537	99.732	0.203	0.2002	0.2455	200.665

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]
-2.508	-1.254		-2.508		8.135

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.833
r_lrange_other	19.832
r_mcangle_it	15.465
r_mcangle_other	15.462
r_scangle_it	13.963
r_scangle_other	13.962
r_dihedral_angle_3_deg	13.49
r_dihedral_angle_6_deg	11.492
r_mcbond_it	9.719
r_mcbond_other	9.719
r_scbond_it	8.465
r_scbond_other	8.463
r_dihedral_angle_1_deg	6.612
r_dihedral_angle_2_deg	2.549
r_angle_refined_deg	0.856
r_angle_other_deg	0.3
r_nbd_refined	0.234
r_nbd_other	0.231
r_symmetry_nbd_refined	0.222
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.039
r_bond_other_d	0.004
r_bond_refined_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	4537
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	21

Software

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