3PTQ

The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNative Os4BGlu12

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5288.1519% PEG 2000, 0.1M Tris HCl, 0.16M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K
Crystal Properties
Matthews coefficientSolvent content
2.6253.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.112α = 90
b = 114.112β = 90
c = 184.541γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0000NSRRCBL13B1

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
12.453099.90.0944.48.643131
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)
12.452.5199.90.494.48.6381316

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 REPLACEMENTTHROUGHOUTNative Os4BGlu122.453043131229299.810.211130.209030.25065RANDOM33.562
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]
0.510.51-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.384
r_dihedral_angle_4_deg20.182
r_dihedral_angle_3_deg17.585
r_dihedral_angle_1_deg7.509
r_mcangle_it2.145
r_scangle_it1.885
r_mcbond_it1.831
r_angle_refined_deg1.264
r_scbond_it1.162
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.384
r_dihedral_angle_4_deg20.182
r_dihedral_angle_3_deg17.585
r_dihedral_angle_1_deg7.509
r_mcangle_it2.145
r_scangle_it1.885
r_mcbond_it1.831
r_angle_refined_deg1.264
r_scbond_it1.162
r_nbtor_refined0.312
r_nbd_refined0.207
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.151
r_metal_ion_refined0.105
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7722
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms79

Software

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