5CZS

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


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 = 73.322α = 90
b = 142.326β = 96.84
c = 74.591γ = 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
12.4274.0699.80.156117.657783
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)
12.422.4797.10.90627.1

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 REPLACEMENTTHROUGHOUT4HSN2.4274.0654228350799.730.194580.191040.24569RANDOM35.26
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]
-1.710.452.65-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.602
r_dihedral_angle_4_deg14.561
r_dihedral_angle_3_deg14.16
r_dihedral_angle_1_deg5.569
r_long_range_B_refined3.998
r_long_range_B_other3.998
r_scangle_other2.087
r_mcangle_it1.965
r_mcangle_other1.965
r_angle_refined_deg1.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.602
r_dihedral_angle_4_deg14.561
r_dihedral_angle_3_deg14.16
r_dihedral_angle_1_deg5.569
r_long_range_B_refined3.998
r_long_range_B_other3.998
r_scangle_other2.087
r_mcangle_it1.965
r_mcangle_other1.965
r_angle_refined_deg1.382
r_scbond_it1.268
r_scbond_other1.268
r_mcbond_it1.185
r_mcbond_other1.184
r_angle_other_deg0.797
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms10439
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms111

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing