1RP0

Crystal Structure of Thi1 protein from Arabidopsis thaliana


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6291TES, magnesium chloride, MES, MPD, heptane-1,2,3-triol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0138.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.356α = 90
b = 133.147β = 90
c = 142.301γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.28269, 0.915013ESRFID29

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
11.670.7199.40.04216.38.26342063420
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6493.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONSADTHROUGHOUT1.670.7116381860207321399.380.1810.140720.139140.17063RANDOM12.736
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]
0.250.52-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.239
r_scangle_it6.216
r_scbond_it4.556
r_mcangle_it3.267
r_mcbond_it2.174
r_angle_refined_deg1.915
r_angle_other_deg1.664
r_symmetry_vdw_other0.318
r_symmetry_vdw_refined0.27
r_nbd_other0.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.239
r_scangle_it6.216
r_scbond_it4.556
r_mcangle_it3.267
r_mcbond_it2.174
r_angle_refined_deg1.915
r_angle_other_deg1.664
r_symmetry_vdw_other0.318
r_symmetry_vdw_refined0.27
r_nbd_other0.263
r_symmetry_hbond_refined0.26
r_nbd_refined0.226
r_xyhbond_nbd_refined0.2
r_chiral_restr0.148
r_nbtor_other0.095
r_metal_ion_refined0.039
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4135
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing