4L12

Crystal structure of EGFP-based Calcium Sensor CatchER complexed with Gd


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OKWPDB ENTRY 2OKW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729851 mM HEPES, pH 7.0, 1 mM beta-mercaptoethanol, 50 mM sodium acetate, 17% PEG4000, 2 mM gadolinium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0559.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.062α = 90
b = 88.334β = 90
c = 118.167γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.785098.30.08514.27.23026030260
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)
11.781.8493.80.1858.76.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2OKW1.7827.133026028732152698.190.19720.19720.196040.21965RANDOM
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.643
r_dihedral_angle_3_deg13.274
r_dihedral_angle_4_deg8.549
r_dihedral_angle_1_deg6.946
r_scangle_it3.705
r_scbond_it2.37
r_angle_refined_deg1.594
r_mcangle_it1.537
r_mcbond_it0.959
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.643
r_dihedral_angle_3_deg13.274
r_dihedral_angle_4_deg8.549
r_dihedral_angle_1_deg6.946
r_scangle_it3.705
r_scbond_it2.37
r_angle_refined_deg1.594
r_mcangle_it1.537
r_mcbond_it0.959
r_nbtor_refined0.304
r_nbd_refined0.249
r_symmetry_vdw_refined0.205
r_metal_ion_refined0.172
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.128
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1842
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms2

Software

Software
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling