X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M6KPDB ENTRY 1M6K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729810% (w/v) PEG 6000, 0.1 M NaCl, 0.05 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.1442.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.919α = 80.9
b = 72.609β = 69.87
c = 73.446γ = 71.44
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1APS21-ID-D

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
11.375094.90.0659.53.4187539
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)
11.371.4291.60.4213.23.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1M6K1.3733.23187539178142937594.750.164760.163160.19581RANDOM21.186
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]
0.73-0.010.280.860.07-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.055
r_dihedral_angle_4_deg20.249
r_dihedral_angle_3_deg13.903
r_dihedral_angle_1_deg6.705
r_scbond_it3.474
r_mcangle_it2.821
r_mcbond_it2.071
r_mcbond_other2.07
r_angle_refined_deg1.66
r_angle_other_deg0.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.055
r_dihedral_angle_4_deg20.249
r_dihedral_angle_3_deg13.903
r_dihedral_angle_1_deg6.705
r_scbond_it3.474
r_mcangle_it2.821
r_mcbond_it2.071
r_mcbond_other2.07
r_angle_refined_deg1.66
r_angle_other_deg0.838
r_chiral_restr0.104
r_gen_planes_refined0.014
r_bond_refined_d0.012
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7884
Nucleic Acid Atoms
Solvent Atoms945
Heterogen Atoms171

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling