X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F3W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529860 mM Succinate (pH 5.5), 5.8 mM sodium pyruvate, 2.4 mM MnCl2, 450 mM KCl, and a range of 18 to 20% PEG 8000, 150 mM Alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6152.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.626α = 95.15
b = 109.014β = 93.45
c = 144.463γ = 112.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 210Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing2005-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.9795NSLSX6A

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
11.6510092.50.07414.83.8508417508417
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)
11.651.7155.260.30.3144.33.3

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 REPLACEMENTTHROUGHOUTIF3W1.6576.475084125084122559092.130.1490.1490.1480.174RANDOM15.493
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.18
r_dihedral_angle_4_deg16.837
r_dihedral_angle_3_deg12.631
r_dihedral_angle_1_deg5
r_scangle_it3.005
r_scbond_it1.799
r_angle_refined_deg1.151
r_mcangle_it0.918
r_mcbond_it0.491
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.18
r_dihedral_angle_4_deg16.837
r_dihedral_angle_3_deg12.631
r_dihedral_angle_1_deg5
r_scangle_it3.005
r_scbond_it1.799
r_angle_refined_deg1.151
r_mcangle_it0.918
r_mcbond_it0.491
r_nbtor_refined0.302
r_nbd_refined0.195
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.113
r_metal_ion_refined0.085
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31708
Nucleic Acid Atoms
Solvent Atoms4794
Heterogen Atoms422

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing