3C04

Structure of the P368G mutant of PMM/PGM from P. aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K35 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5297Na, K tartrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.3547.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.597α = 90
b = 72.251β = 90
c = 92.784γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic2007-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
12.24096.50.09513.93.623903
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)
12.22.2892.50.46623.52230

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 DIFFRACTIONrefinementTHROUGHOUT1K352.24022644122296.060.178240.175970.22134RANDOM32.144
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]
-2.22-1.413.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.849
r_dihedral_angle_4_deg16.595
r_dihedral_angle_3_deg14.88
r_dihedral_angle_1_deg5.898
r_scangle_it2.594
r_scbond_it1.658
r_angle_refined_deg1.362
r_mcangle_it0.964
r_mcbond_it0.592
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.849
r_dihedral_angle_4_deg16.595
r_dihedral_angle_3_deg14.88
r_dihedral_angle_1_deg5.898
r_scangle_it2.594
r_scbond_it1.658
r_angle_refined_deg1.362
r_mcangle_it0.964
r_mcbond_it0.592
r_nbtor_refined0.305
r_nbd_refined0.206
r_symmetry_vdw_refined0.178
r_symmetry_hbond_refined0.177
r_xyhbond_nbd_refined0.154
r_chiral_restr0.087
r_metal_ion_refined0.021
r_bond_refined_d0.012
r_gen_planes_refined0.004
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_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 Atoms3439
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling