X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NM1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0259.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.423α = 90
b = 69.045β = 104.2
c = 56.54γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm1-m Pt/Pd-coated ULE mirror2007-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BM0.9999APS17-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.75094.90.0840.08423.187333569701
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7657.90.4070.4072.22.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NM11.738.127360766174352494.690.143390.140810.19087RANDOM31.627
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]
-0.03-0.08-0.250.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.908
r_dihedral_angle_4_deg18.899
r_dihedral_angle_3_deg13.652
r_sphericity_free12.374
r_sphericity_bonded8.069
r_scangle_it7.828
r_scbond_it6.058
r_dihedral_angle_1_deg4.974
r_mcangle_it4.658
r_rigid_bond_restr3.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.908
r_dihedral_angle_4_deg18.899
r_dihedral_angle_3_deg13.652
r_sphericity_free12.374
r_sphericity_bonded8.069
r_scangle_it7.828
r_scbond_it6.058
r_dihedral_angle_1_deg4.974
r_mcangle_it4.658
r_rigid_bond_restr3.73
r_mcbond_it3.44
r_angle_refined_deg1.365
r_nbtor_refined0.312
r_symmetry_vdw_refined0.227
r_nbd_refined0.211
r_symmetry_hbond_refined0.17
r_xyhbond_nbd_refined0.15
r_chiral_restr0.096
r_metal_ion_refined0.067
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3883
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms113

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling