X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D5CPDB entry 1D5C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100mM TrisHCl, 1M LiCl, 32% (w/v) polyethylene glycol 1000, 3.3mM Nonyl-D-glucoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.008α = 90
b = 124.853β = 107.57
c = 66.162γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.0398ESRFID14-4

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
11.8219.0587.70.0560.03217.441.9485384853825.99
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)
1.821.952.20.2490.1464.33482

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1D5C1.8219.05461214612124281000.208490.208490.204840.27735RANDOM26.728
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.997
r_dihedral_angle_4_deg20.478
r_dihedral_angle_3_deg15.831
r_dihedral_angle_1_deg5.799
r_scangle_it2.835
r_scbond_it1.894
r_angle_refined_deg1.4
r_mcangle_it1.343
r_mcbond_it0.814
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.997
r_dihedral_angle_4_deg20.478
r_dihedral_angle_3_deg15.831
r_dihedral_angle_1_deg5.799
r_scangle_it2.835
r_scbond_it1.894
r_angle_refined_deg1.4
r_mcangle_it1.343
r_mcbond_it0.814
r_nbtor_refined0.306
r_nbd_refined0.207
r_symmetry_vdw_refined0.204
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.167
r_chiral_restr0.088
r_metal_ion_refined0.081
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5194
Nucleic Acid Atoms
Solvent Atoms739
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata scaling
AMoREphasing