6CGL

X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound as-isolated (pH 4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PEM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42980.1 M citric acid (pH 4.0), 1.6 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.6666.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.646α = 90
b = 182.061β = 90
c = 155.333γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03320APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
13.25098.10.2040.2240.0923.45.737370
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.2686.30.6420.7240.3280.7234.3

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 REPLACEMENTTHROUGHOUT1PEM3.25033920170093.470.19980.19720.2523RANDOM74.388
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]
1.44-0.59-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.991
r_dihedral_angle_3_deg13.278
r_dihedral_angle_4_deg11.313
r_dihedral_angle_1_deg5.834
r_angle_refined_deg1.01
r_angle_other_deg0.845
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.991
r_dihedral_angle_3_deg13.278
r_dihedral_angle_4_deg11.313
r_dihedral_angle_1_deg5.834
r_angle_refined_deg1.01
r_angle_other_deg0.845
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10919
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms25

Software

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