3ADJ

Structure of Arabidopsis HYL1 and its molecular implications for miRNA processing


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DI2PDB ENTRY 1DI2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293PEG 400, CaCl2, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.108α = 90
b = 46.108β = 90
c = 33.318γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
134099.70.05619.97132222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.197.90.258.15.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DI2332.62132214199.930.261180.255290.32168RANDOM30.89
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]
-0.36-0.360.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.11
r_dihedral_angle_3_deg19.573
r_dihedral_angle_4_deg19.232
r_dihedral_angle_1_deg6.97
r_scangle_it1.726
r_angle_refined_deg1.627
r_scbond_it1.179
r_mcangle_it0.848
r_mcbond_it0.517
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.11
r_dihedral_angle_3_deg19.573
r_dihedral_angle_4_deg19.232
r_dihedral_angle_1_deg6.97
r_scangle_it1.726
r_angle_refined_deg1.627
r_scbond_it1.179
r_mcangle_it0.848
r_mcbond_it0.517
r_nbtor_refined0.313
r_nbd_refined0.273
r_symmetry_vdw_refined0.254
r_symmetry_hbond_refined0.249
r_xyhbond_nbd_refined0.191
r_chiral_restr0.088
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms547
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms

Software

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