X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NP3PDB entry 1NP3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.50.25 M NaCl, 28 % PEG3350 and 0.1 M Bis-Tris, pH 5.5, strictly anaerobic
Crystal Properties
Matthews coefficientSolvent content
3.665.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.05α = 90
b = 185.05β = 90
c = 185.05γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000, 1.7448SLSX06SA

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
12.582.7699.50.09210.93.572509
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)
12.52.6499.90.5132.63.6

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 1NP32.555.7968666365699.20.196460.193920.24377RANDOM47.799
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined8.146
r_long_range_B_other8.146
r_scangle_other6.203
r_mcangle_it5.639
r_mcangle_other5.639
r_scbond_it3.963
r_scbond_other3.963
r_mcbond_it3.771
r_mcbond_other3.767
r_angle_refined_deg1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined8.146
r_long_range_B_other8.146
r_scangle_other6.203
r_mcangle_it5.639
r_mcangle_other5.639
r_scbond_it3.963
r_scbond_other3.963
r_mcbond_it3.771
r_mcbond_other3.767
r_angle_refined_deg1.72
r_angle_other_deg1.655
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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 Atoms9964
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
SHELXphasing