X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S1CPDB ENTRY 1S1C, partially refined structure of free IpgB2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527720% (w/v) PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3748.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.59α = 90
b = 101.6β = 96.43
c = 97.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
11.8548.2198.40.05215.113.5133487-326.4
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)
11.851.997.80.4922.52.69777

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 1S1C, partially refined structure of free IpgB21.8548.2133481667498.420.180.1770.233RANDOM21.609
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]
-0.45-0.291.47-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.973
r_dihedral_angle_4_deg17.979
r_dihedral_angle_3_deg15.15
r_dihedral_angle_1_deg5.217
r_scangle_it3.45
r_scbond_it2.153
r_angle_refined_deg1.423
r_mcangle_it1.361
r_mcbond_it0.777
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.973
r_dihedral_angle_4_deg17.979
r_dihedral_angle_3_deg15.15
r_dihedral_angle_1_deg5.217
r_scangle_it3.45
r_scbond_it2.153
r_angle_refined_deg1.423
r_mcangle_it1.361
r_mcbond_it0.777
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11613
Nucleic Acid Atoms
Solvent Atoms1766
Heterogen Atoms116

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction