4HSN

Crystal structure of DAH7PS from Neisseria meningitidis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OF8PDB ENTRY 1OF8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.15A protein solution [11 mg/mL in 10 mM BTP buffer (pH 7.3)] was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 15% 20% (w/v) PEG 2000 mme, 0.4 mM MnSO4. The drop sizes were 2 uL, and the volume of the reservoir solution was 500 uL, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4750.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.462α = 90
b = 137.279β = 96.42
c = 76.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1219.7999.3100515100515
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03100

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1OF8219.79100477623399.240.17740.17540.2085RANDOM37.0606
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]
-4.63-0.034.220.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.391
r_dihedral_angle_4_deg20.536
r_dihedral_angle_3_deg14.428
r_dihedral_angle_1_deg5.529
r_angle_refined_deg1.781
r_angle_other_deg1.478
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.391
r_dihedral_angle_4_deg20.536
r_dihedral_angle_3_deg14.428
r_dihedral_angle_1_deg5.529
r_angle_refined_deg1.781
r_angle_other_deg1.478
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.01
r_gen_planes_other0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10432
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms64

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XSCALEdata scaling
Aimlessdata scaling