X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HZDPDB entry (3HZD)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528329% PEG 4000, 0.1M Tris HCl, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Crystal Properties
Matthews coefficientSolvent content
2.1241.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.5α = 90
b = 70.8β = 102.2
c = 43.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirrors2007-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.425LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.555098.20.0670.06712.733.332689-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6299.40.4390.4391.823.2

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 REPLACEMENTTHROUGHOUTPDB entry (3HZD)1.5518.3230990165298.250.202910.200490.24647RANDOM30.019
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.865
r_dihedral_angle_4_deg19.752
r_dihedral_angle_3_deg14.602
r_dihedral_angle_1_deg5.661
r_sphericity_free5.26
r_scangle_it4
r_scbond_it3.864
r_rigid_bond_restr3.805
r_sphericity_bonded2.987
r_mcangle_it1.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.865
r_dihedral_angle_4_deg19.752
r_dihedral_angle_3_deg14.602
r_dihedral_angle_1_deg5.661
r_sphericity_free5.26
r_scangle_it4
r_scbond_it3.864
r_rigid_bond_restr3.805
r_sphericity_bonded2.987
r_mcangle_it1.778
r_angle_refined_deg1.632
r_mcbond_it1.195
r_nbtor_refined0.328
r_nbd_refined0.249
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.145
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms1906
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms82

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling