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Crystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other HUMAN D-XYLULOSE DETERMINED BY TWO-ENERGY SELENIUM MAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 200 MM MES/KOH PH 5.9, 15% (W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.16 α = 90 b = 102.16 β = 90 c = 159.39 γ = 120
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 QUANTUM 315r MIRRORS 2009-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 1.97 36.8 100 0.14 9.8 5.7 131532 -3 37.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2 99.8 0.5 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT HUMAN D-XYLULOSE DETERMINED BY TWO-ENERGY SELENIUM MAD 1.97 36.82 128989 6465 98.1 0.1744 0.1732 0.1972 0.1751 RANDOM 45.83
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] -2.7559 -2.7559 5.5118
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.15 t_other_torsion 2.81 t_angle_deg 1.05 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_omega_torsion 4.15 t_other_torsion 2.81 t_angle_deg 1.05 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 11988 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 95
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing