4Z6J

Crystal structure of apo intact hoefavidin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.5-1.8 M Li2SO4 and 0.1 M HEPES (pH 7.5-7.7)
Crystal Properties
Matthews coefficientSolvent content
2.0540.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.01α = 90
b = 82.01β = 90
c = 130.1γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.96ESRFID29

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
12.45099.60.0413811.110687
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)
12.42.490.227

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 REPLACEMENTTHROUGHOUT3ew12.447.971013152099.620.235150.232490.28945RANDOM48.032
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]
-0.71-0.35-0.712.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.596
r_dihedral_angle_3_deg18.219
r_dihedral_angle_1_deg8.322
r_long_range_B_refined6.973
r_long_range_B_other6.832
r_angle_refined_deg1.657
r_mcangle_it1.647
r_mcangle_other1.646
r_scangle_other1.345
r_angle_other_deg1.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.596
r_dihedral_angle_3_deg18.219
r_dihedral_angle_1_deg8.322
r_long_range_B_refined6.973
r_long_range_B_other6.832
r_angle_refined_deg1.657
r_mcangle_it1.647
r_mcangle_other1.646
r_scangle_other1.345
r_angle_other_deg1.326
r_mcbond_other0.967
r_mcbond_it0.966
r_scbond_it0.782
r_scbond_other0.779
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.004
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1980
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
XSCALEdata scaling