5YJW

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G9K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629350mM Mes(pH 6.0), 34%(v/v) PEG 400, 100mM NaCl, 2% (v/v) ethylene glycol, 5%(v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
359.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.67α = 90
b = 128.456β = 90
c = 86.711γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
11.855099.90.0867.15.449022
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)
11.851.881000.7861.85

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 REPLACEMENTTHROUGHOUT4G9K1.8529.4849008263292.520.183410.182270.2043RANDOM24.261
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]
0.01-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.089
r_dihedral_angle_4_deg15.5
r_dihedral_angle_3_deg13.426
r_long_range_B_refined5.671
r_dihedral_angle_1_deg5.626
r_long_range_B_other5.389
r_scangle_other1.789
r_mcangle_it1.626
r_mcangle_other1.626
r_angle_refined_deg1.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.089
r_dihedral_angle_4_deg15.5
r_dihedral_angle_3_deg13.426
r_long_range_B_refined5.671
r_dihedral_angle_1_deg5.626
r_long_range_B_other5.389
r_scangle_other1.789
r_mcangle_it1.626
r_mcangle_other1.626
r_angle_refined_deg1.443
r_angle_other_deg1.121
r_scbond_it1.043
r_scbond_other1.043
r_mcbond_it0.914
r_mcbond_other0.914
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3578
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms317

Software

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