2ZLG

The Structual Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CVXPDB ENTRY 2CVX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298100mM Hepes, 20-25% PEG3350, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0138.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.789α = 90
b = 116.565β = 90
c = 63.641γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
12.5279.0698.30.07418.84.727055
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)
12.5222.58792.40.4612.43.8

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 2CVX2.5249.625564135997.030.219160.215530.2919RANDOM41.129
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]
-5.59-2.78.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.4
r_dihedral_angle_3_deg18.319
r_dihedral_angle_4_deg15.686
r_scangle_it7.1
r_dihedral_angle_1_deg6.147
r_scbond_it5.412
r_mcangle_it5.176
r_mcbond_it3.845
r_angle_refined_deg1.421
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.4
r_dihedral_angle_3_deg18.319
r_dihedral_angle_4_deg15.686
r_scangle_it7.1
r_dihedral_angle_1_deg6.147
r_scbond_it5.412
r_mcangle_it5.176
r_mcbond_it3.845
r_angle_refined_deg1.421
r_nbtor_refined0.333
r_nbd_refined0.256
r_symmetry_vdw_refined0.24
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.134
r_chiral_restr0.088
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5228
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing