X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YNA2YNA, chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529020.3 mg/mL protein, well solution: 0,1M Hepes pH 7.5, 0.2M proline, 10% w/v polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
3.9368.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.059α = 90
b = 120.391β = 90
c = 138.884γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.975096.40.04740.57107729
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)
11.972.0293.10.7752.25.1

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 REPLACEMENTTHROUGHOUT2YNA, chain A1.9750102185537096.240.194510.192850.22612RANDOM28.459
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]
-0.710.580.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.46
r_dihedral_angle_4_deg20.633
r_dihedral_angle_3_deg13.335
r_dihedral_angle_1_deg6.51
r_scangle_it4.103
r_scbond_it2.61
r_mcangle_it1.794
r_angle_refined_deg1.539
r_mcbond_it1.001
r_angle_other_deg0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.46
r_dihedral_angle_4_deg20.633
r_dihedral_angle_3_deg13.335
r_dihedral_angle_1_deg6.51
r_scangle_it4.103
r_scbond_it2.61
r_mcangle_it1.794
r_angle_refined_deg1.539
r_mcbond_it1.001
r_angle_other_deg0.922
r_mcbond_other0.242
r_chiral_restr0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
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 Atoms6800
Nucleic Acid Atoms
Solvent Atoms758
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement