X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DEFBASED ON MONOMER OF HNP-3 (PDB ENTRY 1DEF)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293lithium sulfate, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.038α = 90
b = 26.051β = 105.79
c = 61.587γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0000APS22-BM

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
11.485095.60.0382071920719
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.5565.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTBASED ON MONOMER OF HNP-3 (PDB ENTRY 1DEF)1.5191904719047102295.60.1790.179210.177340.21252RANDOM26.748
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]
-0.12-0.030.060.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.474
r_dihedral_angle_4_deg17.172
r_dihedral_angle_3_deg11.783
r_sphericity_free9.97
r_dihedral_angle_1_deg7.516
r_sphericity_bonded5.673
r_scangle_it4.267
r_mcangle_it3.976
r_scbond_it3.276
r_mcbond_it2.945
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.474
r_dihedral_angle_4_deg17.172
r_dihedral_angle_3_deg11.783
r_sphericity_free9.97
r_dihedral_angle_1_deg7.516
r_sphericity_bonded5.673
r_scangle_it4.267
r_mcangle_it3.976
r_scbond_it3.276
r_mcbond_it2.945
r_rigid_bond_restr2.467
r_angle_refined_deg2.023
r_symmetry_hbond_refined0.351
r_nbtor_refined0.331
r_symmetry_vdw_refined0.28
r_nbd_refined0.245
r_xyhbond_nbd_refined0.174
r_chiral_restr0.141
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms936
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing