X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TBMPDB ENTRY 1TBM

Crystallization

Crystal Properties
Matthews coefficientSolvent content
4.6673.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.65α = 90
b = 103.65β = 90
c = 270.041γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
12.35098.70.085237652992

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1TBM2.55046414526199.540.198850.195660.22627RANDOM40.023
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]
1.861.86-3.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.991
r_dihedral_angle_4_deg21.603
r_dihedral_angle_3_deg17.57
r_dihedral_angle_1_deg6.529
r_scangle_it4.327
r_scbond_it2.76
r_mcangle_it1.499
r_angle_refined_deg1.35
r_angle_other_deg0.832
r_mcbond_it0.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.991
r_dihedral_angle_4_deg21.603
r_dihedral_angle_3_deg17.57
r_dihedral_angle_1_deg6.529
r_scangle_it4.327
r_scbond_it2.76
r_mcangle_it1.499
r_angle_refined_deg1.35
r_angle_other_deg0.832
r_mcbond_it0.717
r_symmetry_vdw_other0.3
r_symmetry_vdw_refined0.27
r_symmetry_hbond_refined0.268
r_nbd_refined0.262
r_nbd_other0.213
r_xyhbond_nbd_refined0.207
r_metal_ion_refined0.203
r_nbtor_refined0.201
r_mcbond_other0.187
r_nbtor_other0.092
r_chiral_restr0.077
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5412
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement