6GZH | pdb_00006gzh

Crystal Structure of Human CDK9/cyclinT1 with A86

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	7.3	277.15	CDK9/Cyclin T1 at a concentration of 4.5 mg/ml (20 mM Tris / HCl, 250 mM NaCl, 1 mM DTT, 1 mM EDTA, pH 7.3) was pre-incubated with 0.6 mM (5.1-fold molar excess) of A-86 (150 mM in DMSO) and 4 mM TCEP for 1 h. 0.1 ul of the protein solution was then mixed 0.1 ul of reservoir solution (0.01 M Ca-Chloride, 0.1 M MES/NaOH, pH 6.50, 1.2 M Na-Acetate) and equilibrated at 4 C over 0.06 ml of reservoir solution. Crystals were obtained using microseeding. Well diffracting crystals appeared within 4 days and grew to full size over 8 days

Crystal Properties
Matthews coefficient	Solvent content
3.84	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.599	α = 90
b = 171.599	β = 90
c = 97.79	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	100.15	PIXEL	DECTRIS PILATUS3 2M		2017-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	3.17	30	89.7	0.156	3.6	1.5		16344

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.17	3.34	83.7		0.702	1.1	1.4

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	3BLH	3.17	30	15466	857	89.49	0.17497	0.17055	0.18	0.25677	0.26	RANDOM	86.514

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]
-0.36	-0.18		-0.36		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.89
r_dihedral_angle_3_deg	15.414
r_dihedral_angle_4_deg	15.327
r_long_range_B_refined	6.639
r_long_range_B_other	6.569
r_dihedral_angle_1_deg	6.267
r_mcangle_it	3.514
r_mcangle_other	3.514
r_scangle_other	3.252
r_mcbond_it	2.046
r_mcbond_other	2.044
r_scbond_it	1.865
r_scbond_other	1.86
r_angle_refined_deg	1.187
r_angle_other_deg	0.873
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4590
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
REFMAC	phasing