X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RJ5PDB ENTRY 1RJ5, 1JCZ
experimental modelPDB 1JCZPDB ENTRY 1RJ5, 1JCZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.16M MgCl2, 0.08M Tris pH 8.5, 16% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.65α = 90
b = 80.048β = 90
c = 133.441γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDOSMIC2008-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99988SLSX10SA

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
11.943.499.30.0840.0528.63.4441424186222
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)
11.9297.40.5650.3671.93.16197

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 1RJ5, 1JCZ1.941.274414241862222399.220.179460.176520.23536RANDOM17.52
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]
1.13-20.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.393
r_dihedral_angle_4_deg17.365
r_dihedral_angle_3_deg13.876
r_scangle_it8.448
r_dihedral_angle_1_deg6.765
r_scbond_it6.292
r_mcangle_it4.267
r_mcbond_it2.795
r_angle_refined_deg1.562
r_angle_other_deg0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.393
r_dihedral_angle_4_deg17.365
r_dihedral_angle_3_deg13.876
r_scangle_it8.448
r_dihedral_angle_1_deg6.765
r_scbond_it6.292
r_mcangle_it4.267
r_mcbond_it2.795
r_angle_refined_deg1.562
r_angle_other_deg0.93
r_mcbond_other0.816
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3866
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms14

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling