X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LTXPDB ENTRY 1LTX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.228414% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.748α = 90
b = 90.628β = 90
c = 114.068γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.98SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.83099.30.06316.44.66481864333530
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.999.70.2754.73.49571

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LTX1.829.1361099321499.260.151080.148880.19383RANDOM17.742
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_deg37.169
r_dihedral_angle_4_deg19.436
r_dihedral_angle_3_deg15.566
r_dihedral_angle_1_deg5.19
r_scangle_it3.825
r_scbond_it2.411
r_mcangle_it1.86
r_angle_refined_deg1.25
r_mcbond_it1.157
r_mcbond_other0.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.169
r_dihedral_angle_4_deg19.436
r_dihedral_angle_3_deg15.566
r_dihedral_angle_1_deg5.19
r_scangle_it3.825
r_scbond_it2.411
r_mcangle_it1.86
r_angle_refined_deg1.25
r_mcbond_it1.157
r_mcbond_other0.956
r_angle_other_deg0.863
r_nbd_refined0.215
r_symmetry_vdw_other0.202
r_nbd_other0.187
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.159
r_symmetry_vdw_refined0.134
r_symmetry_metal_ion_refined0.116
r_symmetry_hbond_refined0.114
r_metal_ion_refined0.104
r_nbtor_other0.086
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5125
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing