X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J1RPDB entry 2J1R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52942M MgSO4, 100mM Tris, pH 8.5, vapor diffusion, hanging drop, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.2962.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.189α = 90
b = 67.189β = 90
c = 98.322γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2008-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C1.00APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.929.4691.50.09110.515.916856
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9772.30.55613.8

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 2J1R1.9129.461570284490.920.176120.174570.2057RANDOM25.947
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]
-0.57-0.571.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_3_deg13.891
r_dihedral_angle_4_deg8.84
r_dihedral_angle_1_deg6.424
r_scangle_it4.246
r_scbond_it2.519
r_mcangle_it1.677
r_angle_refined_deg1.466
r_mcbond_it0.909
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_3_deg13.891
r_dihedral_angle_4_deg8.84
r_dihedral_angle_1_deg6.424
r_scangle_it4.246
r_scbond_it2.519
r_mcangle_it1.677
r_angle_refined_deg1.466
r_mcbond_it0.909
r_chiral_restr0.133
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms1107
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection