1NB0

Crystal Structure of Human Riboflavin Kinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293NA cadodalyte, Mg acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0639.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.096α = 90
b = 57.096β = 90
c = 82.505γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADEMIRROR2002-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1.0080APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75095.90.03649.212.4717010-320.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7683.20.24.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.749.391584386194.360.1860.1840.221RANDOM15.5
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]
-0.21-0.11-0.210.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.017
r_scangle_it3.779
r_scbond_it2.511
r_mcangle_it1.907
r_angle_refined_deg1.611
r_mcbond_it1.042
r_nbd_refined0.227
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.017
r_scangle_it3.779
r_scbond_it2.511
r_mcangle_it1.907
r_angle_refined_deg1.611
r_mcbond_it1.042
r_nbd_refined0.227
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.158
r_chiral_restr0.12
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1177
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
HKL-2000data reduction