3K8T

Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound


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, PH7.5, 20-25% PEG 3350, 0.2M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.0239.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.528α = 90
b = 116.915β = 90
c = 64.065γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-12MSINGLE WAVELENGTH
21x-rayCCDMARMOSAIC 300 mm CCD2007-03-10MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C
2SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-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
1,22.15099.30.1648.476.947632
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)
1,22.12.1896.80.4232.413.8

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 2CVX2.138.8445193240999.30.2540.2520.29RANDOM50.59
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]
-2.17-1.513.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.829
r_dihedral_angle_3_deg18.786
r_dihedral_angle_4_deg18.205
r_dihedral_angle_1_deg7
r_scangle_it2.799
r_scbond_it2.034
r_angle_refined_deg1.719
r_mcangle_it1.288
r_mcbond_it1.074
r_angle_other_deg0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.829
r_dihedral_angle_3_deg18.786
r_dihedral_angle_4_deg18.205
r_dihedral_angle_1_deg7
r_scangle_it2.799
r_scbond_it2.034
r_angle_refined_deg1.719
r_mcangle_it1.288
r_mcbond_it1.074
r_angle_other_deg0.939
r_xyhbond_nbd_other0.272
r_symmetry_vdw_other0.24
r_mcbond_other0.217
r_nbd_refined0.214
r_nbd_other0.196
r_xyhbond_nbd_refined0.191
r_nbtor_refined0.188
r_symmetry_vdw_refined0.14
r_symmetry_hbond_refined0.127
r_chiral_restr0.113
r_nbtor_other0.092
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5120
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms67

Software

Software
Software NamePurpose
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing