X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E8TPDB ENTRY 3E8T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529150mM MES pH 6.2-6.7, 20-25% PEG 3000, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0840.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.043α = 90
b = 54.051β = 90
c = 83.577γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.534.699.90.110.1111.3749139.7
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)
12.52.6499.80.3890.389211.41055

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 3E8T2.533.06745834499.850.1870.1830.26RANDOM19.626
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]
1.19-0.36-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.942
r_dihedral_angle_3_deg14.401
r_dihedral_angle_4_deg10.907
r_dihedral_angle_1_deg6.748
r_scangle_it2.378
r_scbond_it1.619
r_angle_refined_deg1.408
r_mcangle_it0.936
r_angle_other_deg0.839
r_mcbond_it0.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.942
r_dihedral_angle_3_deg14.401
r_dihedral_angle_4_deg10.907
r_dihedral_angle_1_deg6.748
r_scangle_it2.378
r_scbond_it1.619
r_angle_refined_deg1.408
r_mcangle_it0.936
r_angle_other_deg0.839
r_mcbond_it0.833
r_nbd_refined0.208
r_symmetry_hbond_refined0.185
r_nbtor_refined0.177
r_nbd_other0.174
r_symmetry_vdw_other0.161
r_xyhbond_nbd_refined0.138
r_symmetry_vdw_refined0.132
r_mcbond_other0.108
r_nbtor_other0.087
r_chiral_restr0.074
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1719
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms53

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection