6GZD | pdb_00006gzd

Crystal structure of Human CSNK1A1 with A86

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FQD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277.15	CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days.

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.383	α = 90
b = 113.383	β = 90
c = 80.878	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100.5	PIXEL	DECTRIS PILATUS3 2M		2017-06-23	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	2.28	29.31	98.1	0.07	13.3	4		22991

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	2.28	2.4			0.56

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	5FQD	2.28	29.31	21917	1071	98.01	0.17709	0.17496	0.18	0.22117	0.23	RANDOM	58.303

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]
-0.21			-0.21		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.433
r_dihedral_angle_3_deg	13.346
r_dihedral_angle_4_deg	11.595
r_long_range_B_refined	9.954
r_long_range_B_other	9.949
r_scangle_other	7.515
r_mcangle_it	6.226
r_mcangle_other	6.224
r_dihedral_angle_1_deg	5.586
r_scbond_it	5.056
r_scbond_other	5.055
r_mcbond_it	4.327
r_mcbond_other	4.325
r_angle_other_deg	3.585
r_angle_refined_deg	1.182
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_other	0.006
r_gen_planes_refined	0.004
r_bond_other_d
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	2456
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
REFMAC	phasing
MOSFLM	data reduction