6T29

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)

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, SITTING DROP	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 = 57.82	α = 90
b = 45.64	β = 104.183
c = 108.754	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 6M		2017-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.95372	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.48	55.45	98.7	0.026	0.999	14.8	6.3		44955

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.51	98.3		0.155	0.883	4.2	6.6

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	1.484	55.448	44954	2291	98.465	0.137	0.1355	0.1747	17.818

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]
0.727		-0.17	-0.188		-0.402

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.006
r_dihedral_angle_4_deg	21.923
r_dihedral_angle_3_deg	11.751
r_dihedral_angle_1_deg	6.255
r_lrange_it	3.535
r_lrange_other	3.535
r_scangle_it	2.815
r_scangle_other	2.815
r_mcangle_it	2.324
r_mcangle_other	2.323
r_scbond_it	2.231
r_scbond_other	2.23
r_mcbond_it	1.714
r_mcbond_other	1.713
r_angle_other_deg	1.416
r_angle_refined_deg	1.409
r_rigid_bond_restr	1.4
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.187
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.174
r_nbd_other	0.163
r_symmetry_xyhbond_nbd_refined	0.136
r_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2175
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	73

Software

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