2VQC

Structure of a DNA binding winged-helix protein, F-112, from Sulfolobus Spindle-shaped Virus 1.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6HANGING DROP VAPOR DIFFUSION IN 0.1M MES (PH 6.0). QIUCK SOAK IN ML CONTAINING 25% GLYCEROL AS A CRYOPROTECTANT.
Crystal Properties
Matthews coefficientSolvent content
1.831.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.716α = 90
b = 87.716β = 90
c = 34.491γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2005-04-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.891940, 0.979180, 0.979320SSRLBL9-2

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
12.33099.90.0720.67.744113
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)
12.32.361000.1112.37.3

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 DIFFRACTIONMADTHROUGHOUTNONE2.325.53413323599.90.1750.1730.199RANDOM23.47
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.633
r_dihedral_angle_4_deg17.348
r_dihedral_angle_3_deg12.02
r_dihedral_angle_1_deg4.165
r_scangle_it0.986
r_angle_refined_deg0.923
r_angle_other_deg0.682
r_scbond_it0.667
r_symmetry_vdw_refined0.625
r_mcangle_it0.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.633
r_dihedral_angle_4_deg17.348
r_dihedral_angle_3_deg12.02
r_dihedral_angle_1_deg4.165
r_scangle_it0.986
r_angle_refined_deg0.923
r_angle_other_deg0.682
r_scbond_it0.667
r_symmetry_vdw_refined0.625
r_mcangle_it0.387
r_mcbond_it0.306
r_nbd_refined0.178
r_nbtor_refined0.166
r_nbd_other0.148
r_symmetry_vdw_other0.129
r_xyhbond_nbd_refined0.121
r_symmetry_hbond_refined0.115
r_nbtor_other0.08
r_chiral_restr0.052
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms582
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement