X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPTHE PROTEIN SOLUTION (1.6 MG/ML; 50 MM TRIS-HCL. PH 7) WAS MIXED WITH BIOTIN SOLUTION (1 MG/ML; 5 MM TRIS, PH 8.8, 8 MM CHES, PH 9.5) IN 10:1 V/V RATIO BEFORE CRYSTALLIZATION. SITTING DROPS WITH 300 NL OF PROTEIN-LIGAND SOLUTION AND 150 NL OF WELL SOLUTION (0.18 M MAGNESIUM CHLORIDE, 0.09 M BIS TRIS, PH 5.5, 23% W/V PEG 3350) WERE USED. 30% V/V GLYCEROL IN WELL SOLUTION WAS ADDED TO THE DROP BEFORE FREEZING IN LIQUID NITROGEN.
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.24α = 90
b = 196.84β = 90
c = 52.59γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42012-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.4251000.12148.274935-3
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)
12.42.5990.6138.3

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 1WBI2.424.5871194374199.810.195460.191730.26596RANDOM27.233
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]
1.44-0.78-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_3_deg17.426
r_dihedral_angle_4_deg17.132
r_dihedral_angle_1_deg7.176
r_angle_refined_deg1.749
r_angle_other_deg0.863
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_3_deg17.426
r_dihedral_angle_4_deg17.132
r_dihedral_angle_1_deg7.176
r_angle_refined_deg1.749
r_angle_other_deg0.863
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms14505
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms262

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing