3TY3

Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe bound to glycyl-glycyl-glycine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X0LCHAINSAW MODEL FROM PDB ENTRY 1X0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 3550, Li acetate, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.243α = 90
b = 92.854β = 106.71
c = 75.474γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.852099.50.07213.76.36068160681-3
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)
11.851.8994.70.4153.93836

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 REPLACEMENTTHROUGHOUTCHAINSAW MODEL FROM PDB ENTRY 1X0L1.8519.75973059730303299.630.19480.19480.19280.23RANDOM26.5137
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]
-0.4-0.011-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.442
r_dihedral_angle_4_deg19.317
r_dihedral_angle_3_deg13.258
r_dihedral_angle_1_deg5.526
r_scangle_it3.756
r_scbond_it2.313
r_angle_refined_deg1.413
r_mcangle_it1.347
r_mcbond_it0.778
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.442
r_dihedral_angle_4_deg19.317
r_dihedral_angle_3_deg13.258
r_dihedral_angle_1_deg5.526
r_scangle_it3.756
r_scbond_it2.313
r_angle_refined_deg1.413
r_mcangle_it1.347
r_mcbond_it0.778
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5282
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms50

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing