3AKA

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSe-Met structure of CabD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291PEG 8000, Cacodylate Sodium, Zinc Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0740.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.876α = 90
b = 51.044β = 90
c = 86.998γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.85098.90.05411.94.321409-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.9194.60.3372.83.51683

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSe-Met structure of CabD1.825.22134041340473499.770.2090.199260.196710.24826RANDOM20.116
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]
-0.18-0.770.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.948
r_dihedral_angle_4_deg18.035
r_dihedral_angle_3_deg13.385
r_dihedral_angle_1_deg4.753
r_scangle_it3.391
r_scbond_it2.234
r_angle_refined_deg1.336
r_mcangle_it1.26
r_mcbond_it0.844
r_symmetry_metal_ion_refined0.521
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.948
r_dihedral_angle_4_deg18.035
r_dihedral_angle_3_deg13.385
r_dihedral_angle_1_deg4.753
r_scangle_it3.391
r_scbond_it2.234
r_angle_refined_deg1.336
r_mcangle_it1.26
r_mcbond_it0.844
r_symmetry_metal_ion_refined0.521
r_symmetry_vdw_refined0.462
r_nbtor_refined0.304
r_xyhbond_nbd_refined0.297
r_metal_ion_refined0.272
r_nbd_refined0.23
r_symmetry_hbond_refined0.173
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1224
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms9

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling