2VWD

Nipah Virus Attachment Glycoprotein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1620% (V/V) PEG 6000, 0.1 M MES PH 6.0, 0.1 M LICL AND 0.1 M GAMMA-BUTYLACTONE 18%
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.633α = 90
b = 86.936β = 108.32
c = 82.903γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDMARMOSAIC 225 mm CCDMIRRORS2007-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.25401000.1418.47.345810-3
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)
12.252.331000.8735.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VSM2.2539.9443463232399.80.1750.1720.221RANDOM21.73
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]
0.390.080.86-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.138
r_dihedral_angle_4_deg15.875
r_dihedral_angle_3_deg13.018
r_dihedral_angle_1_deg6.334
r_scangle_it1.611
r_angle_refined_deg1.209
r_scbond_it0.988
r_angle_other_deg0.839
r_mcangle_it0.705
r_mcbond_it0.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.138
r_dihedral_angle_4_deg15.875
r_dihedral_angle_3_deg13.018
r_dihedral_angle_1_deg6.334
r_scangle_it1.611
r_angle_refined_deg1.209
r_scbond_it0.988
r_angle_other_deg0.839
r_mcangle_it0.705
r_mcbond_it0.642
r_nbd_other0.184
r_nbd_refined0.175
r_nbtor_refined0.171
r_symmetry_vdw_other0.159
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.135
r_symmetry_hbond_refined0.132
r_nbtor_other0.093
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6510
Nucleic Acid Atoms
Solvent Atoms578
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing