4FG8 | pdb_00004fg8

Crystal structure of human calcium/calmodulin-dependent protein kinase I 1-315 in complex with ATP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FG7	PDB ENTRY 4FG7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	3% dioxane, 100mM MES, 1.5M (NH4)2SO4, pH 6.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.415	α = 90
b = 83.415	β = 90
c = 153.372	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX315HE		2012-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9791	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	76.7	99.1	0.072	22.4	5.5	30376				43.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	99.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 4FG7	2.2	76.7	30376	30343	1557	98.97	0.1981	0.1954	0.2	0.2484	0.19	RANDOM	54.5095

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.091
r_dihedral_angle_4_deg	19.705
r_dihedral_angle_3_deg	17.019
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	5.994
r_dihedral_angle_1_deg	5.67
SIDE-CHAIN BOND REFINED ATOMS (A''2)	3.699
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	2.894
RIGID-BOND RESTRAINTS (A''2)	2.036
MAIN-CHAIN BOND REFINED ATOMS (A''2)	1.632
r_angle_refined_deg	1.588

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.091
r_dihedral_angle_4_deg	19.705
r_dihedral_angle_3_deg	17.019
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	5.994
r_dihedral_angle_1_deg	5.67
SIDE-CHAIN BOND REFINED ATOMS (A''2)	3.699
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	2.894
RIGID-BOND RESTRAINTS (A''2)	2.036
MAIN-CHAIN BOND REFINED ATOMS (A''2)	1.632
r_angle_refined_deg	1.588
CHIRAL-CENTER RESTRAINTS (A''3)	0.131
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4183
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	62

Software

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

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.