4L13

Crystal structure of Ligand Free EGFP-based Calcium Sensor CatchER


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, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0860.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.401α = 90
b = 88.534β = 90
c = 118.427γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.8APS22-ID

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
11.665099.10.06822.66.73804838048
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)
11.661.7293.60.2287.76.1

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 2OKW1.6631.083804836141190498.830.18250.18250.181390.20323RANDOM
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_deg32.81
r_dihedral_angle_3_deg12.223
r_dihedral_angle_4_deg11.357
r_dihedral_angle_1_deg6.422
r_scangle_it3.684
r_scbond_it2.267
r_angle_refined_deg1.527
r_mcangle_it1.452
r_mcbond_it0.92
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.81
r_dihedral_angle_3_deg12.223
r_dihedral_angle_4_deg11.357
r_dihedral_angle_1_deg6.422
r_scangle_it3.684
r_scbond_it2.267
r_angle_refined_deg1.527
r_mcangle_it1.452
r_mcbond_it0.92
r_nbtor_refined0.303
r_nbd_refined0.247
r_symmetry_vdw_refined0.205
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.107
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1842
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms4

Software

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