2OG3

structure of the rna binding domain of n protein from SARS coronavirus in cubic crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OFZpdb entry 2ofz

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION827740% MPD and 0.1 M Tris pH 8.0, typically crystals appear within 2 weeks, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.665.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.001α = 90
b = 110.001β = 90
c = 110.001γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDmirrors2005-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9797SSRLBL11-1

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
11.8538.999.780.0750.06829.334.1180181798929.19
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)
1.851.891000.470.441.911.91330

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2ofz1.8538.9179891798997699.780.19610.201330.199040.24711RANDOM29.19
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.272
r_dihedral_angle_4_deg22.427
r_dihedral_angle_3_deg16.017
r_dihedral_angle_1_deg6.377
r_scangle_it3.685
r_scbond_it2.292
r_mcangle_it1.658
r_angle_refined_deg1.431
r_mcbond_it1.012
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.272
r_dihedral_angle_4_deg22.427
r_dihedral_angle_3_deg16.017
r_dihedral_angle_1_deg6.377
r_scangle_it3.685
r_scbond_it2.292
r_mcangle_it1.658
r_angle_refined_deg1.431
r_mcbond_it1.012
r_nbtor_refined0.302
r_symmetry_hbond_refined0.262
r_nbd_refined0.207
r_xyhbond_nbd_refined0.197
r_symmetry_vdw_refined0.18
r_chiral_restr0.117
r_metal_ion_refined0.053
r_symmetry_metal_ion_refined0.02
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms889
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing