7OMV

Thermus sp. 2.9 DarT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OMUD_1292116031

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294100 mM potassium thiocyanate, 30% (w/v) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
1.9938.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.317α = 90
b = 90.77β = 90
c = 34.948γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.2990.7796.90.0790.0820.0230.9981511.348391
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.291.310.3680.4060.1660.9342.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUED_12921160311.2945.42648332243996.6580.1630.16140.202219.362
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]
-3.4870.0473.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.804
r_dihedral_angle_4_deg15.658
r_rigid_bond_restr12.695
r_dihedral_angle_3_deg12.676
r_lrange_it8.611
r_dihedral_angle_1_deg6.639
r_lrange_other6.329
r_scangle_other4.632
r_scangle_it4.603
r_scbond_other3.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.804
r_dihedral_angle_4_deg15.658
r_rigid_bond_restr12.695
r_dihedral_angle_3_deg12.676
r_lrange_it8.611
r_dihedral_angle_1_deg6.639
r_lrange_other6.329
r_scangle_other4.632
r_scangle_it4.603
r_scbond_other3.718
r_scbond_it3.645
r_mcangle_it2.657
r_mcangle_other2.656
r_mcbond_other2.324
r_mcbond_it2.321
r_angle_refined_deg1.792
r_angle_other_deg1.432
r_symmetry_xyhbond_nbd_refined0.237
r_nbd_refined0.205
r_symmetry_nbd_other0.181
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.157
r_symmetry_nbd_refined0.138
r_nbd_other0.13
r_chiral_restr0.101
r_symmetry_nbtor_other0.082
r_xyhbond_nbd_other0.016
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1730
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing