3AKA

Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium-binding protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Se-Met structure of CabD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	PEG 8000, Cacodylate Sodium, Zinc Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.876	α = 90
b = 51.044	β = 90
c = 86.998	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	IMAGE PLATE	MAR scanner 345 mm plate		2007-07-31	M	SINGLE WAVELENGTH

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

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	1.8	50	98.9	0.054	11.9	4.3		21409		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.91	94.6		0.337	2.8	3.5	1683

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Se-Met structure of CabD	1.8	25.22	13404	13404	734	99.77	0.209	0.19926	0.19671	0.24826	RANDOM	20.116

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]
-0.18			-0.77		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.948
r_dihedral_angle_4_deg	18.035
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_1_deg	4.753
r_scangle_it	3.391
r_scbond_it	2.234
r_angle_refined_deg	1.336
r_mcangle_it	1.26
r_mcbond_it	0.844
r_symmetry_metal_ion_refined	0.521
r_symmetry_vdw_refined	0.462
r_nbtor_refined	0.304
r_xyhbond_nbd_refined	0.297
r_metal_ion_refined	0.272
r_nbd_refined	0.23
r_symmetry_hbond_refined	0.173
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1224
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling