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
3.2461.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 263.843α = 90
b = 64.939β = 115.16
c = 140.461γ = 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
12.355099.40.098.93.89002353

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 2VX32.3539.8385514449899.70.203960.201780.24582RANDOM50.937
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]
-0.12-0.220.10.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.344
r_dihedral_angle_4_deg19.083
r_dihedral_angle_3_deg14.025
r_long_range_B_refined7.567
r_long_range_B_other7.55
r_dihedral_angle_1_deg6.169
r_scangle_other5.498
r_mcangle_it5.239
r_mcangle_other5.238
r_scbond_it3.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.344
r_dihedral_angle_4_deg19.083
r_dihedral_angle_3_deg14.025
r_long_range_B_refined7.567
r_long_range_B_other7.55
r_dihedral_angle_1_deg6.169
r_scangle_other5.498
r_mcangle_it5.239
r_mcangle_other5.238
r_scbond_it3.556
r_scbond_other3.533
r_mcbond_it3.449
r_mcbond_other3.449
r_angle_refined_deg1.511
r_angle_other_deg0.892
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms10921
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms281

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling