X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W85PDB entry 1w85

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5291.15The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
1.8332.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.673α = 90
b = 232.294β = 91.2
c = 91.936γ = 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 ID14-20.933ESRFID14-2

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
12.357798.90.080.09113.94.21179193.13.1
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)
2.352.4691.90.2270.2655.93.4

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 1w852.3572.17111973111973590698.90.192480.18960.24718RANDOM28.681
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]
2.250.25-0.93-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.564
r_dihedral_angle_1_deg23.503
r_dihedral_angle_4_deg11.301
r_dihedral_angle_3_deg10.493
r_mcangle_it1.953
r_mcbond_it1.686
r_angle_refined_deg1.14
r_scangle_it0.569
r_symmetry_hbond_refined0.448
r_symmetry_vdw_refined0.408
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.564
r_dihedral_angle_1_deg23.503
r_dihedral_angle_4_deg11.301
r_dihedral_angle_3_deg10.493
r_mcangle_it1.953
r_mcbond_it1.686
r_angle_refined_deg1.14
r_scangle_it0.569
r_symmetry_hbond_refined0.448
r_symmetry_vdw_refined0.408
r_scbond_it0.341
r_nbtor_refined0.326
r_nbd_refined0.222
r_xyhbond_nbd_refined0.22
r_symmetry_metal_ion_refined0.211
r_chiral_restr0.17
r_metal_ion_refined0.138
r_bond_refined_d0.007
r_gen_planes_refined0.003
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22043
Nucleic Acid Atoms
Solvent Atoms1127
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing