X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O5PPDB entry 3O5P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729330 % Jeffamine ED-2001, 0.1 M HEPES, pH 7.0, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.978α = 90
b = 47.978β = 90
c = 88.998γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9723SLSX10SA

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
11.341.55999.10.0630.06313.14.12953814.32
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)
11.31.3798.20.3990.3991.83.84215

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 3O5P1.32029516148798.810.17350.17180.2062RANDOM17.7403
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.539
r_dihedral_angle_3_deg13.73
r_dihedral_angle_4_deg9.673
r_sphericity_free8.811
r_dihedral_angle_1_deg7.97
r_sphericity_bonded5.452
r_scangle_it3.993
r_scbond_it3.006
r_mcangle_it2.264
r_mcbond_it1.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.539
r_dihedral_angle_3_deg13.73
r_dihedral_angle_4_deg9.673
r_sphericity_free8.811
r_dihedral_angle_1_deg7.97
r_sphericity_bonded5.452
r_scangle_it3.993
r_scbond_it3.006
r_mcangle_it2.264
r_mcbond_it1.745
r_angle_refined_deg1.554
r_rigid_bond_restr1.473
r_mcbond_other0.912
r_angle_other_deg0.885
r_symmetry_hbond_refined0.282
r_nbd_refined0.281
r_symmetry_vdw_other0.269
r_symmetry_vdw_refined0.268
r_xyhbond_nbd_refined0.221
r_nbd_other0.204
r_nbtor_refined0.181
r_chiral_restr0.092
r_nbtor_other0.087
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms982
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms16

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction