X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GTU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1628020% PEG 4000, pH 6.00, VAPOR DIFFUSION, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.3547.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.965α = 120.53
b = 93.096β = 106.19
c = 92.998γ = 89.97
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.66710097.10.0680.0427.81.938744
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)
2.672.895.10.380.321.71.8

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 REPLACEMENTTHROUGHOUT1GTU2.7203668736687116997.10.2340.2330.264RANDOM54.38
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]
5.56-0.1-0.99-3.49-2.52-5.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.321
r_dihedral_angle_4_deg24.484
r_dihedral_angle_3_deg17.748
r_dihedral_angle_1_deg5.077
r_mcangle_it1.272
r_angle_refined_deg1.17
r_mcbond_it0.739
r_symmetry_hbond_refined0.575
r_scbond_it0.46
r_symmetry_vdw_refined0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.321
r_dihedral_angle_4_deg24.484
r_dihedral_angle_3_deg17.748
r_dihedral_angle_1_deg5.077
r_mcangle_it1.272
r_angle_refined_deg1.17
r_mcbond_it0.739
r_symmetry_hbond_refined0.575
r_scbond_it0.46
r_symmetry_vdw_refined0.41
r_nbtor_refined0.337
r_nbd_refined0.255
r_scangle_it0.252
r_xyhbond_nbd_refined0.183
r_chiral_restr0.082
r_bond_refined_d0.011
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10904
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms210

Software

Software
Software NamePurpose
HKL-2000data reduction
CCP4model building
REFMACrefinement
HKL-2000data scaling
MOLREPphasing