2C1I

Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA) D 275 N Mutant.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C1GPDB ENTRY 2C1G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PROTEIN WAS CRYSTALLIZED FROM 35% PEG 200, 5% PEG 3000, 100 MM MES, PH 6; THEN SOAKED IN 10 MM ZNCL2. FOLLOWED BY SOAK IN 20%PEG 200, 100MM MES, PH 6
Crystal Properties
Matthews coefficientSolvent content
2.243.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.275α = 90
b = 79.239β = 90
c = 100.377γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2004-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.351594.30.0716.85.4933092
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)
11.351.494.50.442.82.7

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 2C1G1.351591377184094.20.1890.1880.225RANDOM20.78
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]
0.44-0.02-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.858
r_dihedral_angle_4_deg18.787
r_dihedral_angle_3_deg14.448
r_dihedral_angle_1_deg6.493
r_scangle_it4.478
r_scbond_it3.345
r_mcangle_it2.366
r_mcbond_it1.697
r_angle_refined_deg1.569
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.858
r_dihedral_angle_4_deg18.787
r_dihedral_angle_3_deg14.448
r_dihedral_angle_1_deg6.493
r_scangle_it4.478
r_scbond_it3.345
r_mcangle_it2.366
r_mcbond_it1.697
r_angle_refined_deg1.569
r_nbtor_refined0.31
r_symmetry_vdw_refined0.228
r_nbd_refined0.216
r_symmetry_hbond_refined0.132
r_chiral_restr0.105
r_xyhbond_nbd_refined0.103
r_bond_refined_d0.016
r_gen_planes_refined0.009
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_mcangle_other
r_scbond_other
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 Atoms3085
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
HKLdata reduction
HKLdata scaling