7ZRQ | pdb_00007zrq

1.68 Angstrom crystal structure of Ca/CaM-E140G: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, HANGING DROP		292	0.1 M Na+-HEPES, 0.1 M MOPS (acid), pH 7.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
	27.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.38	α = 90
b = 54.52	β = 90
c = 57.5	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	1.68	39.59	99.1	0.048	0.057	0.03	1	13.5	6.3		15287

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	1.68	1.71	87.8		2.042	2.522	1.452	0.311	0.6	4.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WEL	1.68	39.59	15244	802	99.084	0.207	0.2052	0.23	0.2439	0.26	29.842

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]
-3.559			0.736		2.823

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.866
r_dihedral_angle_6_deg	15.388
r_dihedral_angle_2_deg	14.283
r_lrange_it	6.752
r_lrange_other	6.736
r_dihedral_angle_1_deg	6.027
r_scangle_it	4.667
r_scangle_other	4.664
r_mcangle_it	3.157
r_mcangle_other	3.155
r_scbond_it	3.076
r_scbond_other	3.074
r_mcbond_it	2.208
r_mcbond_other	2.159
r_angle_refined_deg	1.366
r_symmetry_xyhbond_nbd_refined	0.54
r_angle_other_deg	0.467
r_symmetry_nbd_refined	0.358
r_nbd_refined	0.251
r_nbd_other	0.223
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.182
r_metal_ion_refined	0.169
r_symmetry_metal_ion_refined	0.12
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1288
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	10

Software

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