2O1Z | pdb_00002o1z

Plasmodium vivax Ribonucleotide Reductase Subunit R2 (Pv086155)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HONPDB ENTRY 1HON

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29730% PEG 2K MME, 0.15M Potasium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.1943.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.151α = 90
b = 79.978β = 90
c = 103.846γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Si2006-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.45099.90.1120.1127.96.9255062550638.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.441000.4560.4563.86.71257

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HON2.437.32246352463581699.850.220550.220550.218370.210.285350.28RANDOM31.389
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]
-1.842.72-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.459
r_dihedral_angle_4_deg18.606
r_dihedral_angle_3_deg18.603
r_dihedral_angle_1_deg6.442
r_mcangle_it2.39
r_scangle_it2.061
r_mcbond_it1.51
r_scbond_it1.429
r_angle_refined_deg1.197
r_symmetry_hbond_refined0.371
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4411
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
SOLVEphasing
RESOLVEphasing