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INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH ATP and IP5
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, SITTING DROP 6.25 291 Magnesium chloride, MES, PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.68 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.623 α = 90 b = 140.758 β = 106.53 c = 68.662 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 2015-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979490 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 3.2 70.38 99.3 14.7 6.9 19318
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 3.2 70.38 18378 918 99.16 0.22614 0.22513 0.2277 0.24529 0.2464 RANDOM 102.045
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] 7.11 3.1 -4.73 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.254 r_dihedral_angle_3_deg 15.047 r_dihedral_angle_4_deg 13.882 r_long_range_B_refined 9.211 r_long_range_B_other 9.211 r_mcangle_it 5.872 r_mcangle_other 5.872 r_dihedral_angle_1_deg 5.728 r_scangle_other 5.039 r_mcbond_it 3.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.254 r_dihedral_angle_3_deg 15.047 r_dihedral_angle_4_deg 13.882 r_long_range_B_refined 9.211 r_long_range_B_other 9.211 r_mcangle_it 5.872 r_mcangle_other 5.872 r_dihedral_angle_1_deg 5.728 r_scangle_other 5.039 r_mcbond_it 3.405 r_mcbond_other 3.404 r_scbond_it 2.829 r_scbond_other 2.826 r_angle_refined_deg 1.185 r_angle_other_deg 0.867 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 6574 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Aimless data scaling Coot model building