X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M HEPES pH 7.0, 40 % (v/v) MPD, 5 mM MnCl2, 5 mM bestatin
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.26α = 90
b = 143.45β = 95.54
c = 268.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
12.380.3399.70.0919.13.9290030
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)
12.32.340.5232.13.714130

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 REPLACEMENTTHROUGHOUT5NSK2.380.332756701432299.710.189950.188710.21375RANDOM33.041
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]
2.59-1.71-0.65-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.752
r_dihedral_angle_4_deg14.75
r_dihedral_angle_3_deg13.499
r_dihedral_angle_1_deg5.888
r_long_range_B_refined4.971
r_long_range_B_other4.971
r_scangle_other3.284
r_mcangle_it2.491
r_mcangle_other2.491
r_angle_other_deg2.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.752
r_dihedral_angle_4_deg14.75
r_dihedral_angle_3_deg13.499
r_dihedral_angle_1_deg5.888
r_long_range_B_refined4.971
r_long_range_B_other4.971
r_scangle_other3.284
r_mcangle_it2.491
r_mcangle_other2.491
r_angle_other_deg2.348
r_scbond_it2.161
r_scbond_other2.14
r_mcbond_it1.588
r_mcbond_other1.588
r_angle_refined_deg1.475
r_chiral_restr0.079
r_bond_refined_d0.015
r_bond_other_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.007
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 Atoms45572
Nucleic Acid Atoms
Solvent Atoms2798
Heterogen Atoms436

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing