X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F41PDB ENTRY 1F41

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291Mother liquor: 100 mM tris pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop 1 uL mother liquor + 1 uL TTR 10 mg/mL; crystals appeared in about 5 days, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.169α = 90
b = 86.109β = 90
c = 63.764γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic2005-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.686.10999.90.0460.0468.96.932087320732220.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.691000.3980.3981.96.74565

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1F411.617.873206132042162499.960.1920.1920.1910.218RANDOM21.203
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.885
r_dihedral_angle_4_deg15.355
r_dihedral_angle_3_deg13.435
r_dihedral_angle_1_deg5.758
r_angle_refined_deg1.057
r_nbtor_refined0.301
r_nbd_refined0.181
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.119
r_symmetry_hbond_refined0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.885
r_dihedral_angle_4_deg15.355
r_dihedral_angle_3_deg13.435
r_dihedral_angle_1_deg5.758
r_angle_refined_deg1.057
r_nbtor_refined0.301
r_nbd_refined0.181
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.119
r_symmetry_hbond_refined0.103
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1955
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection