X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YCJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5280PEG8000, ammonium sulfate, phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.872α = 92.69
b = 66.902β = 94.66
c = 90.342γ = 100.82
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMAR CCD 165 mm2006-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.000MAX III911-2

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
11.3589.86294.80.0790.0795.0733.62137892137899.964
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)
11.351.4290.20.3420.3421.73.629699

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 REPLACEMENTTHROUGHOUT1ycj1.3589.8213779209482429794.80.1650.1650.193RANDOM10.008
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]
-0.09-0.010.020.020.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.123
r_dihedral_angle_3_deg10.855
r_dihedral_angle_4_deg9.819
r_dihedral_angle_1_deg5.589
r_sphericity_free3.365
r_scangle_it2.796
r_sphericity_bonded2.112
r_scbond_it2.086
r_mcangle_it1.369
r_mcbond_it1.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.123
r_dihedral_angle_3_deg10.855
r_dihedral_angle_4_deg9.819
r_dihedral_angle_1_deg5.589
r_sphericity_free3.365
r_scangle_it2.796
r_sphericity_bonded2.112
r_scbond_it2.086
r_mcangle_it1.369
r_mcbond_it1.217
r_angle_refined_deg1.174
r_rigid_bond_restr1.087
r_angle_other_deg0.817
r_mcbond_other0.373
r_symmetry_vdw_other0.231
r_nbd_refined0.207
r_nbd_other0.182
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.11
r_symmetry_hbond_refined0.1
r_nbtor_other0.086
r_symmetry_vdw_refined0.082
r_chiral_restr0.072
r_xyhbond_nbd_other0.027
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8069
Nucleic Acid Atoms
Solvent Atoms1441
Heterogen Atoms114

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection