X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IMSPDB Entry 2IMS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6298PEG 3350 15-30% and 0.2 M ammonium fluoride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.247α = 90
b = 53.646β = 114.87
c = 58.074γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic multilayer confocal optics2005-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.48500.0410.04114.73.342100121
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)
11.481.540.2712.71.83

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 2IMS1.4937.3219922107479.470.193930.19250.2201RANDOM23.377
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]
0.2-0.060.21-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.787
r_dihedral_angle_1_deg5.069
r_scbond_it3.555
r_mcangle_it2.217
r_angle_refined_deg1.95
r_mcbond_it1.262
r_angle_other_deg1.038
r_symmetry_hbond_refined0.489
r_symmetry_vdw_other0.276
r_nbd_other0.254
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.787
r_dihedral_angle_1_deg5.069
r_scbond_it3.555
r_mcangle_it2.217
r_angle_refined_deg1.95
r_mcbond_it1.262
r_angle_other_deg1.038
r_symmetry_hbond_refined0.489
r_symmetry_vdw_other0.276
r_nbd_other0.254
r_nbd_refined0.234
r_xyhbond_nbd_refined0.227
r_symmetry_vdw_refined0.206
r_chiral_restr0.127
r_nbtor_other0.095
r_metal_ion_refined0.033
r_bond_refined_d0.027
r_gen_planes_refined0.012
r_gen_planes_other0.011
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms1301
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing