4K2I

Crystal structure of ntda from bacillus subtilis with bound cofactor pmp


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K2BPDB entry 4K2B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62950.1M tri-sodium citrate, 0.2M ammonium acetate, 20% PEG3350, 55mM glutamate, microbatch, pH 5.6, EVAPORATION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5752.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.109α = 90
b = 106.979β = 95.96
c = 99.177γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2011-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
11.7146.899.30.06614.284108740-3
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)
11.711.7598.50.7552.14

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 4K2B2.22537.0321.3418876750673259999.320.16080.15810.2112
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]
-1.25842.5991-3.23214.4905
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.514
f_angle_d1.081
f_chiral_restr0.075
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7008
Nucleic Acid Atoms
Solvent Atoms585
Heterogen Atoms84

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling