3OCC

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PR0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7293150mM DL-malic acid, 20% PEG3350, pH 7.0, EVAPORATION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.647α = 90
b = 109.829β = 90
c = 154.747γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0750NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.75099.50.10.06928.78.11711251711251127.56
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.761000.7240.5492.48816923

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PR01.7501162600162078855499.680.150580.149020.18084RANDOM19.613
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]
-0.661.24-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.239
r_dihedral_angle_4_deg22.232
r_dihedral_angle_3_deg14.451
r_dihedral_angle_1_deg6.649
r_scangle_it4.717
r_scbond_it3.115
r_mcangle_it1.751
r_angle_refined_deg1.519
r_mcbond_it1.058
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.239
r_dihedral_angle_4_deg22.232
r_dihedral_angle_3_deg14.451
r_dihedral_angle_1_deg6.649
r_scangle_it4.717
r_scbond_it3.115
r_mcangle_it1.751
r_angle_refined_deg1.519
r_mcbond_it1.058
r_chiral_restr0.146
r_bond_refined_d0.016
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10788
Nucleic Acid Atoms
Solvent Atoms1170
Heterogen Atoms144

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling