X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VC5PDB ENTRY 2VC5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18TRIS-HCL 50MM PH 8, 15-18% W/V PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.540.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.383α = 90
b = 104.124β = 90
c = 153.051γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.0561.6699.90.1313.667.251419062
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1592.87.1

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 2VC52.0561.6682756437099.90.2390.2370.287RANDOM28.86
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]
0.6-0.17-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.315
r_dihedral_angle_3_deg17.318
r_dihedral_angle_4_deg16.479
r_dihedral_angle_1_deg6.708
r_angle_refined_deg1.119
r_scangle_it0.438
r_mcangle_it0.42
r_nbtor_refined0.297
r_scbond_it0.286
r_mcbond_it0.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.315
r_dihedral_angle_3_deg17.318
r_dihedral_angle_4_deg16.479
r_dihedral_angle_1_deg6.708
r_angle_refined_deg1.119
r_scangle_it0.438
r_mcangle_it0.42
r_nbtor_refined0.297
r_scbond_it0.286
r_mcbond_it0.257
r_nbd_refined0.18
r_symmetry_vdw_refined0.124
r_symmetry_hbond_refined0.116
r_chiral_restr0.104
r_xyhbond_nbd_refined0.088
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms10052
Nucleic Acid Atoms
Solvent Atoms760
Heterogen Atoms348

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing