3M8B

Crystal structure of spin-labeled BtuB V10R1 in the apo state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NQEPDB ENTRY 1NQE, residue 10 deleted

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.62902.5% PEG3350,20 mM Bis Tris, 150 mM Magnesium acetate, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.2562.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.29α = 90
b = 81.29β = 90
c = 226.562γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARMOSAIC 300 mm CCD2009-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

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
12.45092.90.0910.09114.29.632472324726.92
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)
12.42.4938.60.3834.61314

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 1NQE, residue 10 deleted2.4444.133076932415164697.590.2640.2210.2190.248RANDOM30.191
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]
-0.04-0.02-0.040.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.691
r_dihedral_angle_4_deg19.883
r_dihedral_angle_3_deg13.66
r_dihedral_angle_1_deg8.813
r_scangle_it4.978
r_scbond_it3.048
r_mcangle_it1.986
r_angle_refined_deg1.839
r_mcbond_it1.052
r_angle_other_deg0.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.691
r_dihedral_angle_4_deg19.883
r_dihedral_angle_3_deg13.66
r_dihedral_angle_1_deg8.813
r_scangle_it4.978
r_scbond_it3.048
r_mcangle_it1.986
r_angle_refined_deg1.839
r_mcbond_it1.052
r_angle_other_deg0.954
r_mcbond_other0.221
r_chiral_restr0.112
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4329
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms163

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection