X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NWVPDB ENTRY 3NWV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1726-31% (W/V) PEG 1000, 40 MM KH2PO4 PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.346.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.367α = 76.55
b = 53.952β = 88.73
c = 58.95γ = 71.86
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.3530.694.80.078.73.686068-10
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)
11.351.4286.50.422.33.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3NWV1.3530.5981707433894.730.140350.138210.17935RANDOM17.703
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]
0.511.24-1.43-0.13-0.160.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.569
r_sphericity_free32.699
r_dihedral_angle_4_deg18.404
r_sphericity_bonded15.951
r_dihedral_angle_3_deg12.429
r_dihedral_angle_1_deg7.177
r_rigid_bond_restr4.001
r_angle_refined_deg1.99
r_angle_other_deg1.279
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.569
r_sphericity_free32.699
r_dihedral_angle_4_deg18.404
r_sphericity_bonded15.951
r_dihedral_angle_3_deg12.429
r_dihedral_angle_1_deg7.177
r_rigid_bond_restr4.001
r_angle_refined_deg1.99
r_angle_other_deg1.279
r_chiral_restr0.125
r_gen_planes_other0.02
r_bond_refined_d0.017
r_gen_planes_refined0.015
r_bond_other_d0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3260
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling