4IHA

Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5298PEG6000, MPD, pH 7.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.188α = 90
b = 88.729β = 90
c = 118.315γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.00SSRFBL17U

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
11.553099.90.10756.611023322
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)
11.551.7699.80.7796.410931

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 REPLACEMENTTHROUGHOUT1WOM1.553074248537699.760.18270.18130.2011RANDOM20.4594
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]
0.23-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.997
r_dihedral_angle_4_deg14.71
r_dihedral_angle_3_deg12.446
r_dihedral_angle_1_deg5.119
r_scangle_it4.643
r_scbond_it2.867
r_mcangle_it1.964
r_angle_refined_deg1.461
r_mcbond_it1.069
r_angle_other_deg0.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.997
r_dihedral_angle_4_deg14.71
r_dihedral_angle_3_deg12.446
r_dihedral_angle_1_deg5.119
r_scangle_it4.643
r_scbond_it2.867
r_mcangle_it1.964
r_angle_refined_deg1.461
r_mcbond_it1.069
r_angle_other_deg0.892
r_mcbond_other0.289
r_chiral_restr0.086
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4136
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms18

Software

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