5CZ0

Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HSN 

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
2.5451.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.85α = 90
b = 135.25β = 95.95
c = 76.04γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 210r2014-10-23MSINGLE 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
12.575.6397.70.12296.750068
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)
12.52.5697.60.75326.8

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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4HSN2.575.6346903310397.360.204380.200310.263944HSN47.792
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]
-1.030.542.7-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.735
r_dihedral_angle_4_deg15.786
r_dihedral_angle_3_deg14.945
r_dihedral_angle_1_deg5.466
r_long_range_B_refined5.01
r_long_range_B_other5.01
r_mcangle_it3.019
r_mcangle_other3.019
r_scangle_other2.998
r_scbond_it1.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.735
r_dihedral_angle_4_deg15.786
r_dihedral_angle_3_deg14.945
r_dihedral_angle_1_deg5.466
r_long_range_B_refined5.01
r_long_range_B_other5.01
r_mcangle_it3.019
r_mcangle_other3.019
r_scangle_other2.998
r_scbond_it1.822
r_scbond_other1.822
r_mcbond_it1.814
r_mcbond_other1.813
r_angle_refined_deg1.431
r_angle_other_deg0.82
r_chiral_restr0.074
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 Atoms9978
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing