6CKK

N. meningitidis CMP-sialic acid synthetase in the presence of CTP and Ca2+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1 M imidazole pH 8, 6% PEG 8000, and 0.2M calcium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3246.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.19α = 90
b = 69.56β = 90
c = 158.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.03316SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.879.1193.80.0480.99816.643.3542666
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8487.70.2910.923.563.32

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 REPLACEMENTTHROUGHOUT1EYR1.879.1140429217193.740.204350.20190.24958RANDOM22.468
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]
0.260.54-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.957
r_dihedral_angle_3_deg13.578
r_dihedral_angle_4_deg12.357
r_long_range_B_refined7.648
r_long_range_B_other7.572
r_dihedral_angle_1_deg6.285
r_scangle_other4.001
r_mcangle_other3.06
r_mcangle_it3.057
r_scbond_it2.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.957
r_dihedral_angle_3_deg13.578
r_dihedral_angle_4_deg12.357
r_long_range_B_refined7.648
r_long_range_B_other7.572
r_dihedral_angle_1_deg6.285
r_scangle_other4.001
r_mcangle_other3.06
r_mcangle_it3.057
r_scbond_it2.564
r_scbond_other2.563
r_mcbond_it1.948
r_mcbond_other1.928
r_angle_refined_deg1.728
r_angle_other_deg1.026
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3441
Nucleic Acid Atoms
Solvent Atoms680
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing