X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MNV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42940.2 M NaCl 0.1 M Tris HCl pH 7.4 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.262

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.066α = 104.43
b = 116.642β = 104.25
c = 125.17γ = 113.91
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2016-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8723ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.8739.9298.20.1650.997.293.56115590
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.873.050.9240.688

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 REPLACEMENTTHROUGHOUT5MNV2.9339.8988690468484.150.241530.238940.29065RANDOM50.368
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]
0.180.020.08-0.570.110.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.515
r_dihedral_angle_3_deg22.792
r_dihedral_angle_4_deg17.892
r_long_range_B_other11.204
r_long_range_B_refined11.203
r_mcangle_it7.699
r_mcangle_other7.699
r_scangle_other7.228
r_dihedral_angle_1_deg6.597
r_mcbond_it4.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.515
r_dihedral_angle_3_deg22.792
r_dihedral_angle_4_deg17.892
r_long_range_B_other11.204
r_long_range_B_refined11.203
r_mcangle_it7.699
r_mcangle_other7.699
r_scangle_other7.228
r_dihedral_angle_1_deg6.597
r_mcbond_it4.772
r_mcbond_other4.772
r_scbond_it4.385
r_scbond_other4.385
r_angle_refined_deg1.82
r_angle_other_deg1.429
r_chiral_restr0.1
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26350
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms621

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing