4JEB

Crystal structure of an engineered RIDC1 tetramer with four interfacial disulfide bonds and four three-coordinate Zn(II) sites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IQ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529335% methyl-pentandiol, 0.1M HEPES pH 7.5, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7455.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.942α = 90
b = 54.942β = 90
c = 145.658γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDK-B focusing mirrors2012-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.98SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15848.55396.90.0946.55.2134681346822
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)
12.162.2884.90.6920.6921.14.51701

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IQ62.348.55134681137481298.80.24790.24360.3088RANDOM57.6607
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]
2.791.392.79-4.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.469
r_dihedral_angle_4_deg24.698
r_dihedral_angle_3_deg17.708
r_dihedral_angle_1_deg5.196
r_scangle_it3.977
r_scbond_it2.497
r_mcangle_it1.737
r_angle_refined_deg1.56
r_mcbond_it0.916
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.469
r_dihedral_angle_4_deg24.698
r_dihedral_angle_3_deg17.708
r_dihedral_angle_1_deg5.196
r_scangle_it3.977
r_scbond_it2.497
r_mcangle_it1.737
r_angle_refined_deg1.56
r_mcbond_it0.916
r_chiral_restr0.106
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1614
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms89

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
PHASERphasing