X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.2 M potassium/sodium tartrate, 0.1 M sodium citrate, and 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.985α = 90
b = 51.976β = 103.96
c = 38.781γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.92APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
10.913098.20.055167.2938209213113.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
0.910.9482.50.3863.149383

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 REPLACEMENTTHROUGHOUT1MYT0.913087322459498.20.14870.14870.1487RANDOM11.218
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]
-0.12-0.130.33-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.616
r_dihedral_angle_3_deg10.468
r_sphericity_free7.967
r_dihedral_angle_1_deg4.62
r_dihedral_angle_4_deg4.349
r_sphericity_bonded3.781
r_scangle_it3.297
r_scbond_it2.452
r_mcangle_it1.885
r_mcbond_it1.579
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.616
r_dihedral_angle_3_deg10.468
r_sphericity_free7.967
r_dihedral_angle_1_deg4.62
r_dihedral_angle_4_deg4.349
r_sphericity_bonded3.781
r_scangle_it3.297
r_scbond_it2.452
r_mcangle_it1.885
r_mcbond_it1.579
r_rigid_bond_restr1.559
r_angle_refined_deg1.445
r_angle_other_deg0.935
r_mcbond_other0.578
r_nbd_refined0.239
r_nbtor_refined0.181
r_symmetry_vdw_other0.173
r_nbd_other0.161
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.108
r_nbtor_other0.092
r_chiral_restr0.078
r_symmetry_hbond_refined0.059
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1270
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing