X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IT9apo PBP6 model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5292PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.8156.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.534α = 90
b = 185.351β = 100.99
c = 82.329γ = 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 8.3.11.11587ALS8.3.1

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
11.850880.0716.52.2136723
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)
11.81.86840.592.212997

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 REPLACEMENTTHROUGHOUTapo PBP6 model1.840.2136655683187.840.2070.2050.254RANDOM38.923
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]
2.80.27-2.870.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.959
r_dihedral_angle_3_deg19.198
r_dihedral_angle_4_deg18.584
r_dihedral_angle_1_deg14.318
r_scangle_it8.051
r_scbond_it5.261
r_mcangle_it3.512
r_mcbond_it2.29
r_angle_refined_deg1.733
r_chiral_restr0.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.959
r_dihedral_angle_3_deg19.198
r_dihedral_angle_4_deg18.584
r_dihedral_angle_1_deg14.318
r_scangle_it8.051
r_scbond_it5.261
r_mcangle_it3.512
r_mcbond_it2.29
r_angle_refined_deg1.733
r_chiral_restr0.178
r_bond_refined_d0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10613
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms53

Software

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