4BMT

Crystal Structure of Ribonucleotide Reductase di-iron NrdF from Bacillus cereus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BMQPDB ENTRY 4BMQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2 M MG-FORMATE, 20% (W/V) PEG 3350, AND 0.1 M HEPES, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.03α = 90
b = 49.29β = 107.16
c = 98.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.147.188.70.15.72.8297426
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)
12.12.1784.90.32.72.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4BMQ2.147.1128225149888.490.212030.209470.2604RANDOM19.499
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]
0.74-0.580.16-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.065
r_dihedral_angle_4_deg23.083
r_dihedral_angle_3_deg18.997
r_dihedral_angle_1_deg5.924
r_mcangle_it2.382
r_scbond_it2.221
r_angle_refined_deg1.782
r_mcbond_it1.565
r_mcbond_other1.563
r_angle_other_deg1.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.065
r_dihedral_angle_4_deg23.083
r_dihedral_angle_3_deg18.997
r_dihedral_angle_1_deg5.924
r_mcangle_it2.382
r_scbond_it2.221
r_angle_refined_deg1.782
r_mcbond_it1.565
r_mcbond_other1.563
r_angle_other_deg1.332
r_chiral_restr0.129
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4650
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing