X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IT9APO PBP6 STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5292PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.8356.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.938α = 90
b = 185.98β = 101.37
c = 83.036γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM Q315RMIRRORS2009-04-10SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.850950.02819.22.2148355
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)
1.81.8691.80.432.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAPO PBP6 STRUCTURE1.835.81148303730594.80.2050.2030.20.250.25RANDOM40.62
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]
1.11-0.47-1.840.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.193
r_dihedral_angle_4_deg21.141
r_dihedral_angle_3_deg20.143
r_dihedral_angle_1_deg15.563
r_scangle_it9.914
r_scbond_it6.741
r_mcangle_it4.591
r_mcbond_it3.166
r_angle_refined_deg1.322
r_chiral_restr0.114
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10371
Nucleic Acid Atoms
Solvent Atoms774
Heterogen Atoms78

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing