X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B1NPDB ENTRY 3B1N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52930.1M Tris, 0.2M MgCl2, 20% PEG 8000, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4750.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.222α = 90
b = 125.222β = 90
c = 115.002γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
1250990.08314.75.613621328.1
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)
122.111000.4194.35.3

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 3B1N242.35129118705899.80.169160.167280.20398RANDOM22.941
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]
6.316.31-12.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.231
r_dihedral_angle_3_deg18.543
r_dihedral_angle_4_deg17.976
r_dihedral_angle_1_deg6.053
r_scangle_it2.167
r_scbond_it1.417
r_angle_refined_deg1.389
r_mcangle_it0.902
r_mcbond_it0.501
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.231
r_dihedral_angle_3_deg18.543
r_dihedral_angle_4_deg17.976
r_dihedral_angle_1_deg6.053
r_scangle_it2.167
r_scbond_it1.417
r_angle_refined_deg1.389
r_mcangle_it0.902
r_mcbond_it0.501
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms14232
Nucleic Acid Atoms
Solvent Atoms1021
Heterogen Atoms283

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling