X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q9FPDB ENTRY 2Q9F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82918% PEG 8000, 20% glycerol, 50 mM KPi, 0.03% undecylmaltoside, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5952.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.6α = 90
b = 121.6β = 90
c = 143.83γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRh coated flat mirror2009-07-31SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.979SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.392.86990.0650.06553.6458034580348.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.42990.3920.3921.93.56719

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2Q9F2.392.864578743462232598.860.2320.2320.2290.287RANDOM35.1
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]
-1.05-1.052.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.032
r_dihedral_angle_3_deg15.494
r_dihedral_angle_4_deg10.488
r_dihedral_angle_1_deg4.306
r_angle_refined_deg0.854
r_scangle_it0.716
r_scbond_it0.418
r_mcangle_it0.38
r_mcbond_it0.207
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.032
r_dihedral_angle_3_deg15.494
r_dihedral_angle_4_deg10.488
r_dihedral_angle_1_deg4.306
r_angle_refined_deg0.854
r_scangle_it0.716
r_scbond_it0.418
r_mcangle_it0.38
r_mcbond_it0.207
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6836
Nucleic Acid Atoms
Solvent Atoms378
Heterogen Atoms136

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
MOLREPphasing