X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J3VPDB ENTRY 2J3V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1PROTEIN: 14 MG/ML IN H2O RESERVOIR: 0.1 M MES PH 6.1, 2.1 M (NH4)2SO4, 0.03 M COCL2 HANGING DROP 1:1
Crystal Properties
Matthews coefficientSolvent content
2.6653.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.421α = 90
b = 272.898β = 90
c = 246.29γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.269192.80.0423.74.3136331-3
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)
12.262.3677.70.138.8

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 2J3V2.34012981026501000.2010.20.258RANDOM38.4
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]
3.73-0.51-3.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.818
r_dihedral_angle_4_deg20.429
r_dihedral_angle_3_deg17.475
r_dihedral_angle_1_deg6.343
r_scangle_it2.194
r_angle_refined_deg1.603
r_scbond_it1.412
r_mcangle_it0.899
r_mcbond_it0.542
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.818
r_dihedral_angle_4_deg20.429
r_dihedral_angle_3_deg17.475
r_dihedral_angle_1_deg6.343
r_scangle_it2.194
r_angle_refined_deg1.603
r_scbond_it1.412
r_mcangle_it0.899
r_mcbond_it0.542
r_nbtor_refined0.306
r_symmetry_vdw_refined0.258
r_symmetry_hbond_refined0.208
r_nbd_refined0.206
r_xyhbond_nbd_refined0.149
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.004
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_refined
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
r_mcangle_other
r_scbond_other
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 Atoms20631
Nucleic Acid Atoms
Solvent Atoms592
Heterogen Atoms279

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing