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
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.601α = 90
b = 120.384β = 106.57
c = 53.128γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2007-03-14MSINGLE 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
122596.20.1342.62.62317383173811
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)
22.07970.561.12.63

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 1HX12.224.92112190421904184395.770.217270.210050.30384RANDOM48.749
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]
-0.33-0.180.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.11
r_dihedral_angle_3_deg19.048
r_dihedral_angle_4_deg17.874
r_dihedral_angle_1_deg6.877
r_scangle_it2.883
r_scbond_it1.79
r_angle_refined_deg1.636
r_mcangle_it1.204
r_mcbond_it0.691
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.11
r_dihedral_angle_3_deg19.048
r_dihedral_angle_4_deg17.874
r_dihedral_angle_1_deg6.877
r_scangle_it2.883
r_scbond_it1.79
r_angle_refined_deg1.636
r_mcangle_it1.204
r_mcbond_it0.691
r_nbtor_refined0.303
r_nbd_refined0.239
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.188
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3815
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms51

Software

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