X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VX3PDB entry 2vx3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527715% PEG 300, 0.1M LiSO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2161.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 264.097α = 90
b = 65.161β = 115.01
c = 138.426γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97929APS31-ID

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
12.85099.90.0998.93.85311573

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 2vx32.836.7850463265299.920.193270.189910.25754RANDOM53.443
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]
0.72-0.60.08-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.423
r_dihedral_angle_4_deg20.125
r_dihedral_angle_3_deg15.727
r_long_range_B_other8.017
r_long_range_B_refined8.015
r_dihedral_angle_1_deg6.605
r_mcangle_it5.794
r_mcangle_other5.793
r_scangle_other5.705
r_mcbond_it3.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.423
r_dihedral_angle_4_deg20.125
r_dihedral_angle_3_deg15.727
r_long_range_B_other8.017
r_long_range_B_refined8.015
r_dihedral_angle_1_deg6.605
r_mcangle_it5.794
r_mcangle_other5.793
r_scangle_other5.705
r_mcbond_it3.764
r_mcbond_other3.764
r_scbond_it3.656
r_scbond_other3.655
r_angle_refined_deg1.61
r_angle_other_deg0.866
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10918
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms226

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling