2A13

X-ray structure of protein from Arabidopsis thaliana AT1G79260


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827710 MG/ML PROTEIN, 18% PEG2K, 0.025 M TRIS, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.5
2.448.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.056α = 90
b = 80.026β = 90
c = 36.886γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-06-13MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 300 mm CCDHORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR2005-06-13MMAD
31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID
2SYNCHROTRONAPS BEAMLINE 22-ID0.97934, 0.96863APS22-ID

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
1,21.315096.30.06614.917.541019
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)
1.311.3493.193.10.246.1786.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONMADTHROUGHOUT1.3248.0638582206895.40.1570.157080.1560.186RANDOM17.287
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]
0.07-0.10.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.693
r_dihedral_angle_4_deg18.235
r_dihedral_angle_3_deg11.941
r_dihedral_angle_1_deg6.37
r_scangle_it3.552
r_sphericity_free3.111
r_sphericity_bonded3.071
r_scbond_it2.751
r_rigid_bond_restr2.309
r_mcangle_it1.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.693
r_dihedral_angle_4_deg18.235
r_dihedral_angle_3_deg11.941
r_dihedral_angle_1_deg6.37
r_scangle_it3.552
r_sphericity_free3.111
r_sphericity_bonded3.071
r_scbond_it2.751
r_rigid_bond_restr2.309
r_mcangle_it1.834
r_mcbond_it1.329
r_angle_refined_deg1.311
r_nbtor_refined0.292
r_nbd_refined0.192
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.16
r_symmetry_hbond_refined0.109
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1220
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SOLOMONphasing
ARP/wARPmodel building