2WGH

Human Ribonucleotide reductase R1 subunit (RRM1) in complex with dATP and Mg.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZYZPDB ENTRY 1ZYZ

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.2143.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.95α = 90
b = 129.31β = 95.5
c = 76.67γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.34998.40.110.73.856722
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)
12.32.497.70.4533.8

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 1ZYZ2.348.855388428371000.19550.192220.25762RANDOM21.629
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]
1.363.99-2.922.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.283
r_dihedral_angle_4_deg19.263
r_dihedral_angle_3_deg17.692
r_dihedral_angle_1_deg6.722
r_scangle_it3.407
r_scbond_it2.147
r_angle_refined_deg1.613
r_mcangle_it1.367
r_angle_other_deg0.952
r_mcbond_it0.738
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.283
r_dihedral_angle_4_deg19.263
r_dihedral_angle_3_deg17.692
r_dihedral_angle_1_deg6.722
r_scangle_it3.407
r_scbond_it2.147
r_angle_refined_deg1.613
r_mcangle_it1.367
r_angle_other_deg0.952
r_mcbond_it0.738
r_mcbond_other0.161
r_chiral_restr0.094
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10357
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling