7RCZ

Crystal structure of C. difficile SpoVD in complex with ampicillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6UN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29315 % PEG 3350, 0.2 M AmSO4, 10 % PropOH, 0.1 M Na Citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.6954.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.64α = 90
b = 95.62β = 90
c = 176.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97911APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.249.5894.60.1050.1230.0630.9857.33.562415
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)
12.22.2596.80.50.5860.2990.8593.4

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 REPLACEMENTTHROUGHOUT6UN12.249.5859183319293.480.18910.18710.2252RANDOM41.966
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]
-3.231.22.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.918
r_dihedral_angle_3_deg16.096
r_dihedral_angle_4_deg15.13
r_dihedral_angle_1_deg7.123
r_angle_refined_deg1.518
r_angle_other_deg1.216
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.918
r_dihedral_angle_3_deg16.096
r_dihedral_angle_4_deg15.13
r_dihedral_angle_1_deg7.123
r_angle_refined_deg1.518
r_angle_other_deg1.216
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7855
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MoRDaphasing