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INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH IP6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Magnesium Chloride, Sodium Acetate, PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.34 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.55 α = 90 b = 71.637 β = 111.66 c = 61.822 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2016-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 57.46 99.6 13.3 6.6 15186
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 5MW8 2.6 57.46 14393 707 98.99 0.25523 0.25343 0.2562 0.28954 0.2949 RANDOM 68.549
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] 2.91 -12.44 -1.02 6.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_3_deg 17.695 r_dihedral_angle_4_deg 14.903 r_long_range_B_other 7.271 r_long_range_B_refined 7.248 r_dihedral_angle_1_deg 6.29 r_mcangle_it 4.449 r_mcangle_other 4.448 r_scangle_other 3.969 r_mcbond_it 2.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_3_deg 17.695 r_dihedral_angle_4_deg 14.903 r_long_range_B_other 7.271 r_long_range_B_refined 7.248 r_dihedral_angle_1_deg 6.29 r_mcangle_it 4.449 r_mcangle_other 4.448 r_scangle_other 3.969 r_mcbond_it 2.572 r_mcbond_other 2.566 r_scbond_it 2.162 r_scbond_other 2.103 r_angle_refined_deg 1.286 r_angle_other_deg 0.926 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3278 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Aimless data scaling Coot model building