2P3J

Crystal structure of the Arg101Ala mutant protein of Rhesus rotavirus VP8*


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KQRRRV VP8* PDB code 1KQR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.53031.7M (NH4)2SO4, 2.4% v/v PEG 400, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
2.1442.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.531α = 90
b = 48.531β = 90
c = 131.403γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDBRUKER SMART 6000mirrors2004-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE1.5418

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
11.96591.70.04811.812.712064
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)
1.92.04630.1074.71521

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTRRV VP8* PDB code 1KQR1.945.641142158791.670.16290.160750.20586RANDOM18.025
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]
-0.03-0.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.627
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.142
r_dihedral_angle_4_deg2.857
r_scangle_it2.648
r_scbond_it1.786
r_angle_refined_deg1.217
r_mcangle_it1.115
r_mcbond_it0.693
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.627
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.142
r_dihedral_angle_4_deg2.857
r_scangle_it2.648
r_scbond_it1.786
r_angle_refined_deg1.217
r_mcangle_it1.115
r_mcbond_it0.693
r_nbtor_refined0.308
r_nbd_refined0.2
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.133
r_symmetry_hbond_refined0.121
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1274
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
SAINTdata reduction
LSCALEdata scaling
AMoREphasing