X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.83006% PEG 8000, 0.1M sodium dihidrogen phosphate, 0.1M CAPSO pH 9.8, 0.04M spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.7755.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.467α = 90
b = 107.467β = 90
c = 194.772γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
13.49494.80.0851559814806
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)
13.43.5272.20.3741.7

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 1QBK3.449.361480677895.130.23580.232260.30301RANDOM127.231
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]
1.291.29-2.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.291
r_dihedral_angle_3_deg20.613
r_dihedral_angle_4_deg14.001
r_dihedral_angle_1_deg5.141
r_angle_refined_deg1.133
r_scangle_it0.798
r_scbond_it0.457
r_mcangle_it0.446
r_nbtor_refined0.31
r_nbd_refined0.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.291
r_dihedral_angle_3_deg20.613
r_dihedral_angle_4_deg14.001
r_dihedral_angle_1_deg5.141
r_angle_refined_deg1.133
r_scangle_it0.798
r_scbond_it0.457
r_mcangle_it0.446
r_nbtor_refined0.31
r_nbd_refined0.244
r_mcbond_it0.244
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.135
r_chiral_restr0.074
r_symmetry_hbond_refined0.04
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms6652
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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