X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KQRRRV VP8* structure 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
2.1342.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.549α = 90
b = 48.549β = 90
c = 131.639γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDBRUKER SMART 6000mirrors2004-07-01MSINGLE 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
11.7548.5499.70.0638.819.91673116731
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)
1.751.831000.31.92100

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* structure PDB code 1KQR1.75201580584299.980.163880.162620.18773RANDOM14.988
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.201
r_dihedral_angle_3_deg12.296
r_dihedral_angle_4_deg8.704
r_dihedral_angle_1_deg6.145
r_scangle_it3.056
r_scbond_it2.071
r_angle_refined_deg1.304
r_mcangle_it1.253
r_mcbond_it0.788
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.201
r_dihedral_angle_3_deg12.296
r_dihedral_angle_4_deg8.704
r_dihedral_angle_1_deg6.145
r_scangle_it3.056
r_scbond_it2.071
r_angle_refined_deg1.304
r_mcangle_it1.253
r_mcbond_it0.788
r_nbtor_refined0.307
r_nbd_refined0.202
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.111
r_chiral_restr0.09
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1280
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms27

Software

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