X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H7YPDB ENTRY 3H7Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.82880.1M Tris, 10% PEG 8000, 45% MPD, 0.2M NaCl, pH 6.8, Micro batch, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.2745.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.99α = 90
b = 118.493β = 97.92
c = 46.926γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2008-05-22MSINGLE 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
11.87118.6895.50.06715.35.7399492216.884
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)
11.8651.91385.360.5982.75.44989

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 3H7Y1.8726.21223792735905201896.460.186720.184550.184550.22749RANDOM16.884
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]
-0.25-0.610.41-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.836
r_dihedral_angle_4_deg22.411
r_dihedral_angle_3_deg16.852
r_dihedral_angle_1_deg7.289
r_scangle_it5.656
r_scbond_it3.763
r_angle_refined_deg2.205
r_mcangle_it2.024
r_mcbond_it1.183
r_chiral_restr0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.836
r_dihedral_angle_4_deg22.411
r_dihedral_angle_3_deg16.852
r_dihedral_angle_1_deg7.289
r_scangle_it5.656
r_scbond_it3.763
r_angle_refined_deg2.205
r_mcangle_it2.024
r_mcbond_it1.183
r_chiral_restr0.186
r_bond_refined_d0.025
r_gen_planes_refined0.011
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 Atoms3592
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms30

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling