X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TDIPDB ENTRY 1TDI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8HANGING VAPOUR DROP TECHIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 25 MM ANDROSTENE DIONE.
Crystal Properties
Matthews coefficientSolvent content
2.0940.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.177α = 89.76
b = 92.064β = 89.72
c = 113.54γ = 89.73
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2006-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.82094.90.0781.93382191.917.4
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)
11.81.993.60.381.91.9

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 1TDI1.8203048741620894.90.2250.2230.267RANDOM20.44
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]
1.93-0.03-0.08-1.130.23-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.486
r_dihedral_angle_3_deg15.642
r_dihedral_angle_4_deg14.976
r_dihedral_angle_1_deg5.2
r_scangle_it2.008
r_angle_refined_deg1.331
r_scbond_it1.308
r_mcangle_it0.835
r_mcbond_it0.503
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.486
r_dihedral_angle_3_deg15.642
r_dihedral_angle_4_deg14.976
r_dihedral_angle_1_deg5.2
r_scangle_it2.008
r_angle_refined_deg1.331
r_scbond_it1.308
r_mcangle_it0.835
r_mcbond_it0.503
r_nbtor_refined0.304
r_symmetry_vdw_refined0.217
r_nbd_refined0.195
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.154
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms28208
Nucleic Acid Atoms
Solvent Atoms3263
Heterogen Atoms551

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing