X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BLLPDB ENTRY 1BLL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8HANGING DROP BLLAP 7MG/ML IN 50MM TRIS-HCL PH7.8, 50UM ZNSO4, 200MM NACL EQUILIBRATED AGAINST 50MM TRIS-HCL PH7.8, 50UM ZNSO4, 200MM NACL, 50% MPD, pH 7.80
Crystal Properties
Matthews coefficientSolvent content
2.80.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.982α = 90
b = 129.982β = 90
c = 120.813γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.733599.40.0719662705-3
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)
11.731.898.10.473.55.4

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 1BLL1.733559562313599.40.1460.1450.173RANDOM18.69
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]
-0.37-0.18-0.370.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.352
r_dihedral_angle_4_deg17.471
r_dihedral_angle_3_deg12.888
r_dihedral_angle_1_deg6
r_scangle_it5.273
r_scbond_it3.501
r_mcangle_it2.02
r_angle_refined_deg1.59
r_mcbond_it1.389
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.352
r_dihedral_angle_4_deg17.471
r_dihedral_angle_3_deg12.888
r_dihedral_angle_1_deg6
r_scangle_it5.273
r_scbond_it3.501
r_mcangle_it2.02
r_angle_refined_deg1.59
r_mcbond_it1.389
r_nbtor_refined0.31
r_symmetry_vdw_refined0.228
r_nbd_refined0.211
r_symmetry_hbond_refined0.209
r_xyhbond_nbd_refined0.189
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms3746
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling