X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GIZPDB entry 3GIZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429312% PEG3350, 0.1M phosphate citrate pH 4, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6754.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.669α = 61.46
b = 109.545β = 79.29
c = 118.433γ = 87.59
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATEMAR scanner 345 mm plate2007-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97970APS31-ID

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
12.625098.40.05716.8212407812210722
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)
2.622.6998.40.5021.62

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 3GIZ2.6219.96109595574997.020.266860.259440.33904RANDOM48.108
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]
-0.010.020.01-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.852
r_dihedral_angle_3_deg22.564
r_dihedral_angle_4_deg19.771
r_dihedral_angle_1_deg7.981
r_scangle_it2.254
r_angle_refined_deg1.615
r_scbond_it1.306
r_mcangle_it1.167
r_mcbond_it0.626
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.852
r_dihedral_angle_3_deg22.564
r_dihedral_angle_4_deg19.771
r_dihedral_angle_1_deg7.981
r_scangle_it2.254
r_angle_refined_deg1.615
r_scbond_it1.306
r_mcangle_it1.167
r_mcbond_it0.626
r_chiral_restr0.113
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26358
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling