X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GWXPDB entry 3GWX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9298100mM potassium iodide, PEG3500, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9157.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.886α = 90
b = 94.324β = 98.3
c = 97.066γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-06-11MSINGLE 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
12.996.2297.160.073173.4146571465722
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)
12.92.975760.2522852

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 3GWX2.924.012146571465778697.160.218520.217080.24445RANDOM66.22
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]
2.630.513.55-6.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.917
r_dihedral_angle_3_deg15.243
r_dihedral_angle_4_deg13.452
r_dihedral_angle_1_deg4.51
r_scangle_it1.173
r_angle_refined_deg1.048
r_scbond_it0.672
r_mcangle_it0.414
r_nbtor_refined0.302
r_symmetry_vdw_refined0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.917
r_dihedral_angle_3_deg15.243
r_dihedral_angle_4_deg13.452
r_dihedral_angle_1_deg4.51
r_scangle_it1.173
r_angle_refined_deg1.048
r_scbond_it0.672
r_mcangle_it0.414
r_nbtor_refined0.302
r_symmetry_vdw_refined0.259
r_mcbond_it0.229
r_nbd_refined0.197
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.145
r_chiral_restr0.068
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_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 Atoms4064
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement