X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VQ7PDB ENTRY 2VQ7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.520% W/V PEG4000, 100 MM NA-HEPES, 1 MM NADP PH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.2860

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 218.665α = 90
b = 218.665β = 90
c = 130.676γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE 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
12.83099.70.0813.13.286940
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)
12.82.91000.432.13.1

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 2VQ72.829.7282568433299.60.2260.2260.242RANDOM52.87
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]
-1.93-0.96-1.932.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.638
r_dihedral_angle_3_deg19.124
r_dihedral_angle_4_deg17.328
r_dihedral_angle_1_deg6.62
r_scangle_it2.17
r_angle_refined_deg1.432
r_scbond_it1.32
r_mcangle_it0.982
r_mcbond_it0.554
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.638
r_dihedral_angle_3_deg19.124
r_dihedral_angle_4_deg17.328
r_dihedral_angle_1_deg6.62
r_scangle_it2.17
r_angle_refined_deg1.432
r_scbond_it1.32
r_mcangle_it0.982
r_mcbond_it0.554
r_nbtor_refined0.319
r_symmetry_hbond_refined0.298
r_symmetry_vdw_refined0.219
r_nbd_refined0.214
r_xyhbond_nbd_refined0.149
r_chiral_restr0.099
r_bond_refined_d0.012
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 Atoms14552
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms484

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing