X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S1MPDB ENTRY 4S1M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527315%Peg4000, 0.1MTris pH 7.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.1843.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.173α = 90
b = 79.014β = 90
c = 90.697γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.953ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.65099.80.06755.2714.674705-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6399.90.892.3413.63706

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 4S1M1.65074705375199.210.196090.194540.22548RANDOM33.03
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]
2.64-3.050.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.761
r_dihedral_angle_4_deg16.006
r_dihedral_angle_3_deg12.023
r_long_range_B_other7.82
r_long_range_B_refined7.789
r_dihedral_angle_1_deg6.3
r_scangle_other5.723
r_scbond_it4.337
r_scbond_other4.337
r_mcangle_it3.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.761
r_dihedral_angle_4_deg16.006
r_dihedral_angle_3_deg12.023
r_long_range_B_other7.82
r_long_range_B_refined7.789
r_dihedral_angle_1_deg6.3
r_scangle_other5.723
r_scbond_it4.337
r_scbond_other4.337
r_mcangle_it3.398
r_mcangle_other3.398
r_mcbond_it2.396
r_mcbond_other2.395
r_angle_refined_deg2.163
r_angle_other_deg1.642
r_chiral_restr0.138
r_bond_refined_d0.022
r_gen_planes_refined0.013
r_bond_other_d0.01
r_gen_planes_other0.007
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 Atoms4333
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms34

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling