X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528610% PEG 20000, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Crystal Properties
Matthews coefficientSolvent content
2.8957.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.678α = 90
b = 63.243β = 122.15
c = 76.384γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.553096.50.05319.6160631548722
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)
2.552.6479.30.243.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ZB12.5530160791470478396.430.211670.208270.27386RANDOM32.059
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]
-1.281.053.3-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.844
r_dihedral_angle_4_deg22.113
r_dihedral_angle_3_deg20.348
r_dihedral_angle_1_deg6.901
r_scangle_it2.82
r_scbond_it1.78
r_angle_refined_deg1.544
r_mcangle_it1.253
r_mcbond_it0.755
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.844
r_dihedral_angle_4_deg22.113
r_dihedral_angle_3_deg20.348
r_dihedral_angle_1_deg6.901
r_scangle_it2.82
r_scbond_it1.78
r_angle_refined_deg1.544
r_mcangle_it1.253
r_mcbond_it0.755
r_nbtor_refined0.312
r_nbd_refined0.228
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.141
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2828
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection