6T28

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 19 (CS640)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.9	293	0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.64	α = 90
b = 45.62	β = 104.439
c = 108.949	γ = 90

Symmetry
Space Group	I 1 2 1

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 PILATUS 2M		2017-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91840	BESSY	14.2

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	1.55	33.8	86.2	0.996	10.9	4		34389

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	1.55	1.58			0.806

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2jc6	1.55	31.78	34359	1741	85.859	0.159	0.1573	0.1829	19.177

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]
-0.359		-0.702	-0.26		0.866

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.29
r_dihedral_angle_4_deg	18.153
r_dihedral_angle_3_deg	12.889
r_dihedral_angle_1_deg	6.46
r_lrange_it	3.891
r_lrange_other	3.84
r_scangle_it	3.374
r_scangle_other	3.373
r_mcangle_it	3.136
r_mcangle_other	3.135
r_scbond_it	2.834
r_scbond_other	2.833
r_mcbond_it	2.337
r_mcbond_other	2.336
r_rigid_bond_restr	1.865
r_angle_refined_deg	1.436
r_angle_other_deg	1.41
r_nbd_refined	0.21
r_nbd_other	0.192
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.163
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2151
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing