2YV9

Crystal structure of the CLIC homologue EXC-4 from c. elegans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K0M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729315% PEG 3350, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.913α = 90
b = 91.395β = 99.61
c = 63.286γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMARRESEARCHOSMIC MIRRORS2004-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.616.6375.80.040.0416.73.656143227
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6975.80.520.522.53.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1K0M1.616.6157443304274.60.190.1880.235RANDOM28.48
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]
0.240.07-0.260.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.402
r_dihedral_angle_4_deg22.291
r_dihedral_angle_3_deg13.341
r_scangle_it9.579
r_scbond_it7.398
r_mcangle_it6.559
r_mcbond_it5.762
r_dihedral_angle_1_deg5.103
r_mcbond_other1.74
r_angle_refined_deg1.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.402
r_dihedral_angle_4_deg22.291
r_dihedral_angle_3_deg13.341
r_scangle_it9.579
r_scbond_it7.398
r_mcangle_it6.559
r_mcbond_it5.762
r_dihedral_angle_1_deg5.103
r_mcbond_other1.74
r_angle_refined_deg1.456
r_angle_other_deg0.914
r_nbd_refined0.227
r_symmetry_hbond_refined0.227
r_symmetry_vdw_other0.217
r_nbd_other0.188
r_nbtor_refined0.184
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.135
r_chiral_restr0.09
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4555
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms2

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling