X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VL8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.629120% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1141.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.368α = 90
b = 62.368β = 90
c = 226.037γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2001-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

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
12.55096.90.10811.941588422
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)
12.52.5991.90.3823.13.51450

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 REPLACEMENTTHROUGHOUT3VL82.548.092158641506380197.140.188490.185740.2421RANDOM17.941
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]
0.450.45-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.536
r_dihedral_angle_3_deg15.206
r_dihedral_angle_1_deg7.594
r_dihedral_angle_4_deg6.48
r_long_range_B_refined3.59
r_long_range_B_other3.587
r_scangle_other2.558
r_mcangle_it1.975
r_mcangle_other1.975
r_angle_refined_deg1.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.536
r_dihedral_angle_3_deg15.206
r_dihedral_angle_1_deg7.594
r_dihedral_angle_4_deg6.48
r_long_range_B_refined3.59
r_long_range_B_other3.587
r_scangle_other2.558
r_mcangle_it1.975
r_mcangle_other1.975
r_angle_refined_deg1.645
r_scbond_it1.635
r_scbond_other1.574
r_mcbond_it1.182
r_mcbond_other1.179
r_angle_other_deg0.79
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3331
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms10

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling