X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XYHPDB ENTRY 1XYH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72963.2 M NaCl, 0.1 M Bis-Tris propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
4.471.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.399α = 90
b = 132.399β = 90
c = 132.399γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVariMax2005-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
12.546.81000.1370.1376.138.8143181431842.1
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)
2.52.541000.8420.8425.439.4681

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XYH2.546.813563135637181000.192180.192180.189740.24247RANDOM32.127
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.659
r_dihedral_angle_4_deg21.622
r_dihedral_angle_3_deg16.693
r_dihedral_angle_1_deg7.565
r_scangle_it4.32
r_scbond_it2.752
r_angle_refined_deg2.003
r_mcangle_it1.735
r_mcbond_it1.007
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.659
r_dihedral_angle_4_deg21.622
r_dihedral_angle_3_deg16.693
r_dihedral_angle_1_deg7.565
r_scangle_it4.32
r_scbond_it2.752
r_angle_refined_deg2.003
r_mcangle_it1.735
r_mcbond_it1.007
r_nbtor_refined0.328
r_symmetry_vdw_refined0.231
r_nbd_refined0.22
r_xyhbond_nbd_refined0.148
r_chiral_restr0.129
r_symmetry_hbond_refined0.127
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1346
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
PHASERphasing
Omodel building