X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8CHOPDB ENTRY 8CHO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop7.22981.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.274α = 90
b = 64.274β = 90
c = 504.199γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-03-25SINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 325 mm CCD2010-01-05SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2
2SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
1,21.96129.34898.60.1421411.74576645766
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.9612.0791.10.8020.8020.870.3116.85946

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 8CHO1.96129.3441851221995.170.22620.223360.28184RANDOM24.452
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]
0.90.450.9-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.005
r_dihedral_angle_4_deg19.239
r_dihedral_angle_3_deg15.295
r_dihedral_angle_1_deg6.695
r_scangle_it4.725
r_scbond_it3.17
r_mcangle_it2.06
r_angle_refined_deg2.049
r_mcbond_it1.231
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.005
r_dihedral_angle_4_deg19.239
r_dihedral_angle_3_deg15.295
r_dihedral_angle_1_deg6.695
r_scangle_it4.725
r_scbond_it3.17
r_mcangle_it2.06
r_angle_refined_deg2.049
r_mcbond_it1.231
r_chiral_restr0.135
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms3776
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms159

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
Web-Icedata collection
XDSdata reduction