X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X8YPDB ENTRY 2X8Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100 MM HEPES 1.3 M SODIUM CITRATE, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.271

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.125α = 90
b = 173.125β = 90
c = 101.673γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.9750960.099.22.389919
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)
11.91.9783.20.422.31.8

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 2X8Y1.9986.5672831384798.410.181320.180350.19987RANDOM29.318
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]
-2.43-1.22-2.433.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_4_deg15.816
r_dihedral_angle_3_deg12.022
r_dihedral_angle_1_deg4.618
r_scangle_it1.335
r_angle_refined_deg0.914
r_scbond_it0.76
r_mcangle_it0.454
r_mcbond_it0.223
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_4_deg15.816
r_dihedral_angle_3_deg12.022
r_dihedral_angle_1_deg4.618
r_scangle_it1.335
r_angle_refined_deg0.914
r_scbond_it0.76
r_mcangle_it0.454
r_mcbond_it0.223
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4903
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
TRUNCATEdata scaling
PHASERphasing