4PC4

Bombyx mori lipoprotein 6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629310% isopropanol, 10% PEG 3350, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
2.6253.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.21α = 90
b = 85.75β = 104.84
c = 104.47γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976PETRA III, EMBL c/o DESYP14 (MX2)

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
11.847.0594.90.04822.326.44124752123486
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)
11.81.9730.553.485.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.847123486126594.940.161470.161260.18264RANDOM27.053
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]
-0.3-0.36-0.270.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.688
r_dihedral_angle_4_deg14.991
r_dihedral_angle_3_deg12.679
r_long_range_B_refined7.333
r_long_range_B_other7.333
r_dihedral_angle_1_deg6.529
r_scangle_other4.041
r_mcangle_it2.741
r_mcangle_other2.741
r_scbond_it2.641
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.688
r_dihedral_angle_4_deg14.991
r_dihedral_angle_3_deg12.679
r_long_range_B_refined7.333
r_long_range_B_other7.333
r_dihedral_angle_1_deg6.529
r_scangle_other4.041
r_mcangle_it2.741
r_mcangle_other2.741
r_scbond_it2.641
r_scbond_other2.637
r_mcbond_it1.858
r_mcbond_other1.856
r_angle_refined_deg1.528
r_angle_other_deg1.489
r_chiral_restr0.097
r_bond_refined_d0.013
r_bond_other_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.007
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 Atoms9779
Nucleic Acid Atoms
Solvent Atoms1131
Heterogen Atoms87

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement