2E3U

Crystal structure analysis of Dim2p from Pyrococcus horikoshii OT3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22939% PEG 3000, 0.1M cacodylate buffer, 0.2M Magnesium Chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.949α = 90
b = 47.45β = 90
c = 95.722γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12501419934.7

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 REPLACEMENTTHROUGHOUT1TUA2.347.84913546798.180.229260.227560.26258RANDOM25.972
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]
2.261.33-3.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.636
r_dihedral_angle_4_deg18.369
r_dihedral_angle_3_deg17.835
r_dihedral_angle_1_deg5.997
r_scangle_it3.574
r_scbond_it2.223
r_angle_refined_deg1.466
r_mcangle_it1.374
r_mcbond_it0.839
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.636
r_dihedral_angle_4_deg18.369
r_dihedral_angle_3_deg17.835
r_dihedral_angle_1_deg5.997
r_scangle_it3.574
r_scbond_it2.223
r_angle_refined_deg1.466
r_mcangle_it1.374
r_mcbond_it0.839
r_nbtor_refined0.301
r_nbd_refined0.213
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.144
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1320
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms

Software

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