X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LUSPDB ENTRY 4LUS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.17M LiSO4, 0.085M Tris-HCL pH 8.5, 25.5% PEG4000, 15.5% Glycerol, 0.02% betamercaptoethanol, 10 mM PLP , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.97α = 90
b = 154.33β = 113.63
c = 55.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2013-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.645.59970.0974.82.3225862192422
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)
12.62.7455.70.1581.92.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4LUS2.628.832258621910118297.130.184980.181330.25199RANDOM40.878
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]
-13.725.2413.240.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.749
r_dihedral_angle_4_deg23.187
r_long_range_B_refined6.764
r_long_range_B_other6.747
r_mcangle_other4.287
r_scangle_other4.263
r_mcangle_it4.056
r_scbond_it3.145
r_mcbond_other2.724
r_mcbond_it2.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.749
r_dihedral_angle_4_deg23.187
r_long_range_B_refined6.764
r_long_range_B_other6.747
r_mcangle_other4.287
r_scangle_other4.263
r_mcangle_it4.056
r_scbond_it3.145
r_mcbond_other2.724
r_mcbond_it2.706
r_scbond_other2.669
r_angle_refined_deg1.577
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_3_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 Atoms6072
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling