X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HX1PDB ENRTY 1HX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529315% PEG3350, 0.1M Tris buffer, 25mM sodium-potassium tartrate, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.576α = 90
b = 120.827β = 106.62
c = 53.519γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2008-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.92595.80.1274.84.17371863718611
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)
1.91.9787.20.541.14.01

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENRTY 1HX1225112979629796247496.880.218380.2140.27158RANDOM31.728
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]
-0.6-0.69-0.260.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.282
r_dihedral_angle_4_deg19.208
r_dihedral_angle_3_deg16.857
r_dihedral_angle_1_deg5.741
r_scangle_it2.59
r_scbond_it1.653
r_angle_refined_deg1.272
r_mcangle_it1.123
r_mcbond_it0.651
r_nbtor_refined0.292
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.282
r_dihedral_angle_4_deg19.208
r_dihedral_angle_3_deg16.857
r_dihedral_angle_1_deg5.741
r_scangle_it2.59
r_scbond_it1.653
r_angle_refined_deg1.272
r_mcangle_it1.123
r_mcbond_it0.651
r_nbtor_refined0.292
r_symmetry_vdw_refined0.209
r_nbd_refined0.197
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.146
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3806
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms20

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling