X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HX1PDB ENTRY 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
2.2445.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.289α = 90
b = 121.123β = 106.25
c = 52.773γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2006-08-14MSINGLE 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
1224.8798.20.1143.33.9321453214511
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)
22.0797.40.5391.23.96

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 ENTRY 1HX12.224.87112235022350185998.380.20740.200490.29235RANDOM37.924
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]
-2.43-1.22-1.483.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.497
r_dihedral_angle_4_deg20.948
r_dihedral_angle_3_deg19.157
r_dihedral_angle_1_deg6.356
r_scangle_it3.356
r_scbond_it2.081
r_angle_refined_deg1.648
r_mcangle_it1.293
r_mcbond_it0.753
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.497
r_dihedral_angle_4_deg20.948
r_dihedral_angle_3_deg19.157
r_dihedral_angle_1_deg6.356
r_scangle_it3.356
r_scbond_it2.081
r_angle_refined_deg1.648
r_mcangle_it1.293
r_mcbond_it0.753
r_nbtor_refined0.303
r_nbd_refined0.234
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.199
r_xyhbond_nbd_refined0.188
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3798
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms31

Software

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