X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IIDPDB entry 3IID

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62940.8 M (NH4)2SO4, 0.2 M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.160.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.61α = 90
b = 129.61β = 90
c = 128.29γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.164.8299.70.074145.14673046730-337
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1696.20.4823.24.13651

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 3IID2.164.824438923371000.18130.180050.20459RANDOM29.855
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]
0.060.030.06-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.768
r_dihedral_angle_4_deg20.638
r_dihedral_angle_3_deg17.558
r_dihedral_angle_1_deg8.018
r_scangle_it2.883
r_scbond_it1.952
r_angle_refined_deg1.662
r_mcangle_it1.068
r_angle_other_deg1.021
r_mcbond_it0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.768
r_dihedral_angle_4_deg20.638
r_dihedral_angle_3_deg17.558
r_dihedral_angle_1_deg8.018
r_scangle_it2.883
r_scbond_it1.952
r_angle_refined_deg1.662
r_mcangle_it1.068
r_angle_other_deg1.021
r_mcbond_it0.84
r_nbd_refined0.212
r_symmetry_vdw_other0.204
r_symmetry_hbond_refined0.192
r_nbd_other0.185
r_nbtor_refined0.176
r_mcbond_other0.162
r_xyhbond_nbd_refined0.157
r_symmetry_vdw_refined0.133
r_chiral_restr0.096
r_nbtor_other0.09
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4101
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms108

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling