X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M8WPDB ENTRY 3M8W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529313% PEG3350, 50 mM manganese chloride, 75 mM ammonium acetate, 100 mM Bis-Tris, crystals soaked in reservoir solution + 10 mM dideoxyribose 5-phosphate for 30 minutes, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5551.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.504α = 90
b = 76.52β = 108.76
c = 107.286γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15096.70.08318.279568-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1888.70.2833.2

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 3M8W2.1207794175281390196.450.195570.19340.23905RANDOM24.991
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]
1.28-0.52-1.710.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.74
r_dihedral_angle_4_deg14.836
r_dihedral_angle_3_deg14.152
r_dihedral_angle_1_deg5.617
r_angle_refined_deg1.239
r_mcangle_it1.005
r_scbond_it1.002
r_mcbond_it0.585
r_chiral_restr0.079
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.74
r_dihedral_angle_4_deg14.836
r_dihedral_angle_3_deg14.152
r_dihedral_angle_1_deg5.617
r_angle_refined_deg1.239
r_mcangle_it1.005
r_scbond_it1.002
r_mcbond_it0.585
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9196
Nucleic Acid Atoms
Solvent Atoms680
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing