1KHW

Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Mn2+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEG 8000, sodium HEPES, manganese chloride glycerol, hexanediol, 3'-deoxy-ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9257.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.694α = 90
b = 119.845β = 90
c = 159.498γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATERIGAKU RAXIS IVOsmic mirrors2001-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.74099.90.0970.09717.45.83796337963-3-369
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)
12.72.81000.7220.7222.45.53733

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.731.16380163416537951000.2410.240810.237890.26747RANDOM28.407
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]
1.5-2.070.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.422
r_scangle_it4.119
r_dihedral_angle_1_deg3.161
r_scbond_it2.623
r_mcangle_it1.905
r_angle_refined_deg1.426
r_mcbond_it1.116
r_nbd_refined0.166
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.422
r_scangle_it4.119
r_dihedral_angle_1_deg3.161
r_scbond_it2.623
r_mcangle_it1.905
r_angle_refined_deg1.426
r_mcbond_it1.116
r_nbd_refined0.166
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.128
r_chiral_restr0.099
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7776
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing