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Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BO1 PDB ENTRY 1BO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M MAGNESIUM FORMATE, 16% PEG3350, 2 MM BENZYL(1,3,5)TRIPHOSPHATE, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.51 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.04 α = 90 b = 98.508 β = 93.43 c = 104.879 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 CCD ADSC CCD 2010-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.56 28.47 98.1 0.09 7.9 3.7 28302 -3 55.66
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 2.56 2.7 96.8 0.68 1.1 3.6
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 1BO1 2.56 28.37 28285 1444 97.94 0.1907 0.1881 0.202 0.2383 0.258 RANDOM 49.11
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] 15.5792 -4.0507 -21.349 5.7697
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.21 t_omega_torsion 2.96 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.21 t_omega_torsion 2.96 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5210 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 5
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing