X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G4EPDB ENTRY 3G4E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.829838% PEG 6000, 0.1M Tris-Hcl, 5mM DTT, 5mM CaCl2, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.365α = 90
b = 52.019β = 100.11
c = 85.832γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

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
11.9284.52990.0860.0865.251742805
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)
1.922.02940.0130.012860.56.3

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 3G4E1.9284.524273840630210899.230.225190.223720.25336RANDOM43.462
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]
1.91.661.08-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.287
r_sphericity_free26.875
r_sphericity_bonded24.469
r_dihedral_angle_4_deg21.239
r_dihedral_angle_3_deg18.166
r_dihedral_angle_1_deg11.38
r_scangle_it7.244
r_scbond_it5.525
r_rigid_bond_restr4.497
r_mcangle_it4.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.287
r_sphericity_free26.875
r_sphericity_bonded24.469
r_dihedral_angle_4_deg21.239
r_dihedral_angle_3_deg18.166
r_dihedral_angle_1_deg11.38
r_scangle_it7.244
r_scbond_it5.525
r_rigid_bond_restr4.497
r_mcangle_it4.362
r_mcbond_it3.287
r_angle_refined_deg2.582
r_nbtor_refined0.314
r_symmetry_vdw_refined0.291
r_nbd_refined0.261
r_symmetry_hbond_refined0.196
r_chiral_restr0.184
r_xyhbond_nbd_refined0.176
r_bond_refined_d0.035
r_gen_planes_refined0.013
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4606
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms2

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction