2J9O

Structure of PBP-A, L158E mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING DROP. PROTEIN 7 MG/ML. RESERVOIR, 500 UL HEPES 0.1M PH 7.5, AMMONIUM ACETATE 0.2M, PEG-3350 25% (W/V), NAN3 0.02% (W/V). DROP 1UL PROTEIN AND 1 UL RESERVOIR
Crystal Properties
Matthew coefficientSolvent content
2.2746

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.611α = 90
b = 91.462β = 90
c = 145.585γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRROR 1, FLAT PRE-MIRROR. MIRROR 2, BENT, VERTICALLY FOCUSSING2005-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.52598.10.0417.63.4181250
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)
11.51.5599.30.532.43.3

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.525172152909798.10.1790.1770.213RANDOM17.19
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]
0.76-0.52-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.991
r_dihedral_angle_4_deg17.056
r_dihedral_angle_3_deg12.969
r_dihedral_angle_1_deg5.829
r_scangle_it3.82
r_scbond_it2.726
r_angle_refined_deg1.646
r_mcangle_it1.469
r_mcbond_it1.302
r_angle_other_deg1.036
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.991
r_dihedral_angle_4_deg17.056
r_dihedral_angle_3_deg12.969
r_dihedral_angle_1_deg5.829
r_scangle_it3.82
r_scbond_it2.726
r_angle_refined_deg1.646
r_mcangle_it1.469
r_mcbond_it1.302
r_angle_other_deg1.036
r_symmetry_vdw_other0.335
r_mcbond_other0.298
r_nbd_refined0.225
r_nbd_other0.207
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.176
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.16
r_chiral_restr0.099
r_nbtor_other0.089
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_mcangle_other
r_symmetry_hbond_other
r_scbond_other
r_metal_ion_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 Atoms8233
Nucleic Acid Atoms
Solvent Atoms1527
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling