3HNE

Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HNCPDB entry 3HNC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.92980.1 M Tris-HCl pH 7.9, 0.2 M LiSO4, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.147α = 90
b = 114.372β = 90
c = 222.474γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.9000APS23-ID-B

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
135091.70.1319.7556.632613
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)
33.1193.80.6576

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 REPLACEMENTTHROUGHOUTPDB entry 3HNC3.1144.0727243144088.490.189150.184730.27459RANDOM65.226
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]
0.81-1.981.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.422
r_dihedral_angle_3_deg22.243
r_dihedral_angle_4_deg18.708
r_dihedral_angle_1_deg6.844
r_scangle_it2.149
r_angle_refined_deg1.672
r_scbond_it1.294
r_mcangle_it0.901
r_mcbond_it0.481
r_metal_ion_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.422
r_dihedral_angle_3_deg22.243
r_dihedral_angle_4_deg18.708
r_dihedral_angle_1_deg6.844
r_scangle_it2.149
r_angle_refined_deg1.672
r_scbond_it1.294
r_mcangle_it0.901
r_mcbond_it0.481
r_metal_ion_refined0.341
r_nbtor_refined0.321
r_nbd_refined0.249
r_symmetry_vdw_refined0.248
r_symmetry_hbond_refined0.238
r_xyhbond_nbd_refined0.185
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11205
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms123

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection