2HQQ

Crystal structure of human ketohexokinase complexed to different sugar molecules


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RKDPDB ENTRY 1RKD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.72910.7M ammonium sulphate, 0.5M lithium sulphate, 0.1M sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.7567.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.26α = 90
b = 109.619β = 90
c = 146.29γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2003-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.9795SRSPX14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8687.70699.80.0630.0636.67.3416814168127.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.861.9699.20.3250.32557.36030

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSingle Isomorphous ReplacementTHROUGHOUTPDB ENTRY 1RKD1.8687.714179537359412999.270.207680.204740.23384RANDOM26.285
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]
-0.021.38-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.599
r_dihedral_angle_4_deg18.067
r_dihedral_angle_3_deg13.294
r_dihedral_angle_1_deg5.434
r_mcangle_it2.03
r_scangle_it2.026
r_mcbond_it1.764
r_scbond_it1.349
r_angle_refined_deg1.296
r_angle_other_deg0.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.599
r_dihedral_angle_4_deg18.067
r_dihedral_angle_3_deg13.294
r_dihedral_angle_1_deg5.434
r_mcangle_it2.03
r_scangle_it2.026
r_mcbond_it1.764
r_scbond_it1.349
r_angle_refined_deg1.296
r_angle_other_deg0.702
r_mcbond_other0.284
r_symmetry_vdw_other0.27
r_nbd_refined0.217
r_xyhbond_nbd_refined0.212
r_nbd_other0.203
r_symmetry_hbond_refined0.2
r_nbtor_refined0.188
r_symmetry_vdw_refined0.132
r_nbtor_other0.088
r_chiral_restr0.075
r_xyhbond_nbd_other0.065
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2277
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing