5CZT

Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu176Ala variant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.32960.1M Tris HCl (pH 7.3), 0.2 M trimethyl-amino-N-oxide (TMAO), 0.4 mM MnSO4 and PEG 2000MME
Crystal Properties
Matthews coefficientSolvent content
2.6854.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.647α = 90
b = 140.828β = 98.56
c = 77.266γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 210r2015-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.954Australian SynchrotronMX1

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
12.0476.4199.90.07918.67.6101442
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)
12.042.0898.70.6962.67.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.0476.4195084632299.890.172820.170570.20566RANDOM31.738
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]
0.16-0.631.23-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.985
r_dihedral_angle_4_deg14.86
r_dihedral_angle_3_deg13.592
r_dihedral_angle_1_deg5.557
r_long_range_B_refined5.029
r_long_range_B_other5.029
r_scangle_other2.614
r_mcangle_it2.03
r_mcangle_other2.029
r_scbond_it1.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.985
r_dihedral_angle_4_deg14.86
r_dihedral_angle_3_deg13.592
r_dihedral_angle_1_deg5.557
r_long_range_B_refined5.029
r_long_range_B_other5.029
r_scangle_other2.614
r_mcangle_it2.03
r_mcangle_other2.029
r_scbond_it1.664
r_scbond_other1.664
r_angle_refined_deg1.391
r_mcbond_it1.284
r_mcbond_other1.284
r_angle_other_deg0.807
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10503
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing