7ZRP

2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	200 mM Zinc acetate, 100 mM Imidazole pH8.0, 18% PEG3000

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.283	α = 90
b = 72.59	β = 90
c = 78.156	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 XE 16M		2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.65	53.25	100	0.154	0.185	0.102	0.996	5.9	5.8		11133

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.78			1.921	2.3	1.249	0.576		6.1

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WEL	2.65	53.244	11092	555	99.964	0.21	0.2071	0.2724	RANDOM	66.088

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]
-1.179			2.633		-1.454

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.503
r_dihedral_angle_6_deg	14.513
r_dihedral_angle_2_deg	13.784
r_lrange_it	11.564
r_lrange_other	11.528
r_scangle_it	9.107
r_scangle_other	9.104
r_mcangle_it	7.674
r_mcangle_other	7.673
r_scbond_it	6.137
r_scbond_other	6.135
r_dihedral_angle_1_deg	5.851
r_mcbond_it	5.191
r_mcbond_other	5.186
r_angle_refined_deg	1.288
r_angle_other_deg	0.461
r_symmetry_xyhbond_nbd_refined	0.239
r_xyhbond_nbd_refined	0.228
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.216
r_symmetry_nbd_other	0.188
r_nbd_other	0.176
r_nbtor_refined	0.174
r_ncsr_local_group_2	0.129
r_ncsr_local_group_1	0.098
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.059
r_symmetry_metal_ion_refined	0.037
r_metal_ion_refined	0.014
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2636
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	47

Software

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