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Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XAL PDB ENTRY 2XAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 22% PEG 3350, 100 MM BIS-TRIS PH 5.9, 2 MM MGCL2. PROTEIN WAS MIXED WITH 2 MM ADP AND 2 MM INOSITOL-6-P
Crystal Properties Matthews coefficient Solvent content 2.3 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.124 α = 90 b = 113.591 β = 90 c = 142.478 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC QUANTUM 210 2008-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.73 71.24 99.8 0.14 3.84 7.05 48686 2 35.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.4 0.53 1.36 5.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XAL 2.2 88.736 48621 2474 99.782 0.229 0.2266 0.2259 0.2695 0.2625 RANDOM 23.12
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] -0.269 -0.82 1.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.386 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 16.072 r_dihedral_angle_1_deg 5.209 r_scangle_it 2.146 r_scbond_it 1.281 r_angle_refined_deg 1.149 r_mcangle_it 0.951 r_mcbond_it 0.497 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.386 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 16.072 r_dihedral_angle_1_deg 5.209 r_scangle_it 2.146 r_scbond_it 1.281 r_angle_refined_deg 1.149 r_mcangle_it 0.951 r_mcbond_it 0.497 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6694 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing