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 193K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.943α = 90
b = 51.932β = 103.75
c = 38.899γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92Osmic2006-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.093098.40.06118.16.154705513878.2
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)
11.091.1398.40.3653.33.55466

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 REPLACEMENTTHROUGHOUT1MYT1.093051131268498.360.134290.133170.15654RANDOM8.522
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]
0.250.06-0.12-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.041
r_dihedral_angle_4_deg10.76
r_dihedral_angle_3_deg10.732
r_dihedral_angle_1_deg9.043
r_sphericity_free8.401
r_sphericity_bonded3.516
r_scangle_it3.45
r_scbond_it2.74
r_mcangle_it1.992
r_mcbond_it1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.041
r_dihedral_angle_4_deg10.76
r_dihedral_angle_3_deg10.732
r_dihedral_angle_1_deg9.043
r_sphericity_free8.401
r_sphericity_bonded3.516
r_scangle_it3.45
r_scbond_it2.74
r_mcangle_it1.992
r_mcbond_it1.7
r_angle_refined_deg1.541
r_rigid_bond_restr1.376
r_angle_other_deg0.966
r_mcbond_other0.662
r_nbd_refined0.237
r_nbtor_refined0.2
r_nbd_other0.175
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_other0.164
r_symmetry_hbond_refined0.118
r_symmetry_vdw_refined0.117
r_nbtor_other0.089
r_chiral_restr0.084
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1097
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing