7KL2 | pdb_00007kl2

Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VZK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.15 M DL-Malic acid pH 7, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.777	α = 90
b = 65.162	β = 95.8
c = 54.105	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 R 200K-A	Rigaku VariMax HF	2019-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.55	50	99.5	0.199	0.238	0.138	3.2	3.1		9973

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	2.55	2.59	97.7		0.133		2.6

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 (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	6VZK	2.56	41.53	9458	500	98.33	0.2466	0.2439	0.25	0.293	0.3	RANDOM	45.386

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]
-2.02		0.88	-0.85		2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.029
r_dihedral_angle_3_deg	21.391
r_dihedral_angle_4_deg	13.83
r_dihedral_angle_1_deg	7.455
r_angle_refined_deg	1.439
r_angle_other_deg	1.14
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.029
r_dihedral_angle_3_deg	21.391
r_dihedral_angle_4_deg	13.83
r_dihedral_angle_1_deg	7.455
r_angle_refined_deg	1.439
r_angle_other_deg	1.14
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2239
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.