5C40

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FV7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M sodium HEPES, 10% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1843.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.79α = 90
b = 72.42β = 90.43
c = 92.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9789NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.527.1299.20.06211.73.79611812.297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5498.40.6431.93.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FV71.527.1291278482699.160.129310.126590.18132RANDOM20.356
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]
0.40.12-0.25-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.777
r_sphericity_free27.063
r_dihedral_angle_4_deg17.527
r_dihedral_angle_3_deg11.931
r_sphericity_bonded10.744
r_rigid_bond_restr6.618
r_dihedral_angle_1_deg6.002
r_long_range_B_refined4.442
r_scangle_other4.18
r_scbond_it3.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.777
r_sphericity_free27.063
r_dihedral_angle_4_deg17.527
r_dihedral_angle_3_deg11.931
r_sphericity_bonded10.744
r_rigid_bond_restr6.618
r_dihedral_angle_1_deg6.002
r_long_range_B_refined4.442
r_scangle_other4.18
r_scbond_it3.965
r_long_range_B_other3.943
r_scbond_other3.938
r_mcangle_other2.904
r_mcangle_it2.894
r_mcbond_other2.564
r_mcbond_it2.557
r_angle_refined_deg2.324
r_angle_other_deg1.856
r_chiral_restr0.154
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d0.012
r_gen_planes_other0.007
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4620
Nucleic Acid Atoms
Solvent Atoms711
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing