X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IYQPDB ENTRY 2IYQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5170MM NA ACETATE, 15%(V/V) GLYCEROL, 25.5%(W/V) PEG 4000, 85MM TRIS-HCL PH 8.5
Crystal Properties
Matthews coefficientSolvent content
1.832

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.444α = 90
b = 41.836β = 113.99
c = 44.408γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.9819.5496.10.15.972.219559
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)
11.982.0392.90.611.482

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 2IYQ1.9841.851857398696.10.1690.1650.25RANDOM27.61
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]
-0.76-0.030.630.87-0.780.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.321
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg17.104
r_scangle_it11.432
r_scbond_it8.883
r_dihedral_angle_1_deg5.842
r_mcangle_it5.246
r_mcbond_it4.745
r_angle_refined_deg1.597
r_angle_other_deg0.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.321
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg17.104
r_scangle_it11.432
r_scbond_it8.883
r_dihedral_angle_1_deg5.842
r_mcangle_it5.246
r_mcbond_it4.745
r_angle_refined_deg1.597
r_angle_other_deg0.885
r_symmetry_vdw_other0.293
r_symmetry_hbond_refined0.229
r_nbd_refined0.225
r_nbd_other0.201
r_xyhbond_nbd_refined0.187
r_symmetry_vdw_refined0.183
r_nbtor_refined0.169
r_chiral_restr0.09
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms2457
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing