3EKE

Crystal structure of IBV X-domain at pH 5.6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6285.150.8 M AMMONIUM SULFATE, 0.1 M NA-CITRATE PH 5.6, 0.2 M K-,NA-TARTRATE, TEMPERATURE 285.15 K
Crystal Properties
Matthews coefficientSolvent content
3.7166.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.2α = 90
b = 78.2β = 90
c = 81.701γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.167.7398.40.0790.0796.34111.51712332.3
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)
2.12.2189.40.4010.4011.910.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.167.731610217103100199.20.2010.1990.231RANDOM32.92
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]
1.510.751.51-2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.012
r_dihedral_angle_3_deg16.102
r_dihedral_angle_4_deg15.176
r_dihedral_angle_1_deg7.16
r_scangle_it3.811
r_scbond_it2.816
r_angle_refined_deg1.896
r_mcangle_it1.892
r_mcbond_it1.576
r_angle_other_deg1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.012
r_dihedral_angle_3_deg16.102
r_dihedral_angle_4_deg15.176
r_dihedral_angle_1_deg7.16
r_scangle_it3.811
r_scbond_it2.816
r_angle_refined_deg1.896
r_mcangle_it1.892
r_mcbond_it1.576
r_angle_other_deg1.07
r_mcbond_other0.277
r_nbd_refined0.217
r_nbd_other0.207
r_nbtor_refined0.197
r_symmetry_vdw_other0.195
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.148
r_chiral_restr0.133
r_symmetry_vdw_refined0.116
r_nbtor_other0.1
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1330
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms20

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing