3H5R

Crystal structure of E. coli MccB + Succinimide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291.224-26% pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Bis-Tris pH 6.5, 50 mM (NH4)2SO4, 10 mM Succinimidyl peptide, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Crystal Properties
Matthews coefficientSolvent content
1.9236.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.934α = 90
b = 137.972β = 92.1
c = 80.134γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDSagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2008-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00000APS22-BM

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
12.15099.90.0922.1814.4714407144037
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)
12.12.1899.90.5464.2

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 3H5N2.127.9570567355399.880.196580.193750.24995RANDOM45.108
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]
1-0.35-1.330.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.757
r_dihedral_angle_4_deg19.005
r_dihedral_angle_3_deg17.778
r_dihedral_angle_1_deg6.405
r_scangle_it3.252
r_scbond_it2.247
r_angle_refined_deg1.518
r_mcangle_it1.378
r_mcbond_it0.92
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.757
r_dihedral_angle_4_deg19.005
r_dihedral_angle_3_deg17.778
r_dihedral_angle_1_deg6.405
r_scangle_it3.252
r_scbond_it2.247
r_angle_refined_deg1.518
r_mcangle_it1.378
r_mcbond_it0.92
r_nbtor_refined0.312
r_symmetry_vdw_refined0.248
r_nbd_refined0.218
r_xyhbond_nbd_refined0.183
r_symmetry_hbond_refined0.142
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10435
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms14

Software

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