X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529330% MPD, 100 mM Tris pH 8.5, 500 mM Sodium chloride, 8% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5752.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.13α = 90
b = 149.597β = 102.07
c = 147.315γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDRAYONIX MX300HE2016-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.755098.40.0910.10.03810.95.2356244
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.78960.4440.5230.270.173.2

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 REPLACEMENTTHROUGHOUT5GSM1.75303382311796398.030.151610.147970.21995RANDOM34.453
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]
2.362.73-4.450.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.13
r_dihedral_angle_4_deg19.095
r_dihedral_angle_3_deg17.072
r_rigid_bond_restr14.128
r_long_range_B_refined8.449
r_long_range_B_other8.391
r_scangle_other8.1
r_dihedral_angle_1_deg7.511
r_scbond_it7.113
r_scbond_other7.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.13
r_dihedral_angle_4_deg19.095
r_dihedral_angle_3_deg17.072
r_rigid_bond_restr14.128
r_long_range_B_refined8.449
r_long_range_B_other8.391
r_scangle_other8.1
r_dihedral_angle_1_deg7.511
r_scbond_it7.113
r_scbond_other7.113
r_mcangle_it6.804
r_mcangle_other6.804
r_mcbond_it5.758
r_mcbond_other5.755
r_angle_refined_deg1.862
r_angle_other_deg1.66
r_chiral_restr0.093
r_bond_other_d0.017
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.008
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25252
Nucleic Acid Atoms
Solvent Atoms1956
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXmodel building
HKL-2000data reduction