4DS7 | pdb_00004ds7

Crystal structure of yeast calmodulin bound to the C-terminal fragment of spindle pole body protein Spc110

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HR4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	293	0.1M sodium acetate, 0.7M ammonium sulfate, 0.5M guanidine chloride, 0.001M strontium chloride, 0.00005M copper chloride, pH 4.5, 0.0005M LAURYLDIMETHYLAMINE OXIDE, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.67	α = 90
b = 145.444	β = 90
c = 49.837	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 315		2011-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97153	APS	19-ID

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	2.15	30	99.9	0.07	31.184	15.9	47122	47075		-3	41.57

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	2.15	2.19	99.5		3.876	11.7	2321

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 (All)	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	3HR4	2.15	30	46323	46203	2346	99.87	0.1992	0.1992	0.197	0.2	0.2401	0.24	RANDOM	44.8885

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]
-1.03			-0.41		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.953
r_dihedral_angle_4_deg	16.285
r_dihedral_angle_3_deg	15.982
r_scangle_it	6.677
r_dihedral_angle_1_deg	4.262
r_scbond_it	4.031
r_mcangle_it	3.439
r_mcbond_it	1.745
r_angle_refined_deg	0.984
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.953
r_dihedral_angle_4_deg	16.285
r_dihedral_angle_3_deg	15.982
r_scangle_it	6.677
r_dihedral_angle_1_deg	4.262
r_scbond_it	4.031
r_mcangle_it	3.439
r_mcbond_it	1.745
r_angle_refined_deg	0.984
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5629
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	37

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
HKL-3000	data reduction
HKL-3000	data scaling

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.