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Crystal structure of Arabidopsis thaliana PII bound to malonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O66 pdb entry 2O66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.5 M malonate, 0.1 M Na HEPES, pH 7.0, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.594 α = 90 b = 66.726 β = 118.41 c = 61.489 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Osmic multilayer 2006-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 20 99.7 0.104 0.104 14.2 4.6 11464 11464 -3 41.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 98.2 0.517 0.517 2.4 4 1139
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2O66 2.5 20 10903 10903 552 99.63 0.20401 0.20401 0.20088 0.26567 0.2298 RANDOM 44.622
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] 1.45 0.43 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.437 r_dihedral_angle_3_deg 17.08 r_dihedral_angle_4_deg 16.985 r_scangle_it 5.268 r_dihedral_angle_1_deg 5.15 r_scbond_it 3.43 r_mcangle_it 2.64 r_mcbond_it 1.713 r_angle_refined_deg 1.039 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.437 r_dihedral_angle_3_deg 17.08 r_dihedral_angle_4_deg 16.985 r_scangle_it 5.268 r_dihedral_angle_1_deg 5.15 r_scbond_it 3.43 r_mcangle_it 2.64 r_mcbond_it 1.713 r_angle_refined_deg 1.039 r_nbtor_refined 0.297 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_refined 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 Atoms Number Protein Atoms 2477 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing