X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O6YPDB ENTRY 1O6Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62911.2M NaAcetate 50mM NaCacodylate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.4264.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.863α = 90
b = 116.863β = 90
c = 260.347γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.8969.8463.47281952819511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.893.2116

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 1O6Y2.8969.842668526685142668.130.220970.217840.27798RANDOM79.784
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]
3.913.91-7.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.069
r_dihedral_angle_3_deg24.322
r_dihedral_angle_4_deg20.695
r_dihedral_angle_1_deg7.212
r_scangle_it2.074
r_angle_refined_deg1.737
r_scbond_it1.14
r_mcangle_it0.566
r_nbtor_refined0.325
r_mcbond_it0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.069
r_dihedral_angle_3_deg24.322
r_dihedral_angle_4_deg20.695
r_dihedral_angle_1_deg7.212
r_scangle_it2.074
r_angle_refined_deg1.737
r_scbond_it1.14
r_mcangle_it0.566
r_nbtor_refined0.325
r_mcbond_it0.319
r_nbd_refined0.266
r_symmetry_vdw_refined0.244
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.181
r_chiral_restr0.127
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 Atoms7870
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing