X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TVBPDB entry 1TVB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277PEG3350 24%, MES 0.025M, NaCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3246.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.957α = 90
b = 58.369β = 109.66
c = 89.425γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

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
11.92096.40.10714.2365376630021115.6
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)
11.91.9787.90.4632.52.45674

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1TVB1.92016537059801318396.350.190220.187330.24427RANDOM15.408
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]
0.470.6-1.731.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.283
r_dihedral_angle_3_deg17.108
r_dihedral_angle_4_deg15.936
r_dihedral_angle_1_deg6.538
r_scangle_it4.912
r_scbond_it3.097
r_mcangle_it1.842
r_angle_refined_deg1.764
r_mcbond_it0.992
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.283
r_dihedral_angle_3_deg17.108
r_dihedral_angle_4_deg15.936
r_dihedral_angle_1_deg6.538
r_scangle_it4.912
r_scbond_it3.097
r_mcangle_it1.842
r_angle_refined_deg1.764
r_mcbond_it0.992
r_nbtor_refined0.314
r_xyhbond_nbd_refined0.206
r_symmetry_hbond_refined0.196
r_nbd_refined0.157
r_chiral_restr0.137
r_metal_ion_refined0.133
r_symmetry_vdw_refined0.113
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6282
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
MOLREPphasing