X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QD0PDB entry 2QD0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291Crystals were grown by mixing 1 microliter of mitoNEET 23.3 mg/mL in 50 mM Tris HCl, 0.3 M NaCl, pH 8.5 with 1 microliter of 0.1 M Tris HCl, 1.5 ~ 1.8 M ammonium sulfate, pH 8.5 solution against the same solution. Crystals were appeared in 3 days and flash frozen by transfering into 0.1 M Tris HCl, 1.5 ~ 1.8 M amomnium acete, pH 8.5, 20% xylitol for a few minutes, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.968.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.64α = 90
b = 58.64β = 90
c = 177.61γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.7655.68499.80.07813.76.91583115831
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)
11.761.861000.5140.5141.56.62257

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 2QD01.7629.32158561576678999.230.20320.20320.20190.2285RANDOM28.5501
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.897
r_dihedral_angle_3_deg17.471
r_dihedral_angle_4_deg15.316
r_dihedral_angle_1_deg7.26
r_scangle_it6.228
r_scbond_it3.97
r_mcangle_it2.791
r_angle_refined_deg2.57
r_mcbond_it1.849
r_angle_other_deg1.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.897
r_dihedral_angle_3_deg17.471
r_dihedral_angle_4_deg15.316
r_dihedral_angle_1_deg7.26
r_scangle_it6.228
r_scbond_it3.97
r_mcangle_it2.791
r_angle_refined_deg2.57
r_mcbond_it1.849
r_angle_other_deg1.146
r_mcbond_other0.583
r_chiral_restr0.168
r_bond_refined_d0.034
r_gen_planes_refined0.016
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms610
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms4

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection