4IXX

Crystal structure of S213G variant DAH7PS without Tyr bound from Neisseria meningitidis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HSOPDB ENTRY 4HSO

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, temperature 293.15K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3347.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.064α = 90
b = 132.432β = 95.72
c = 75.028γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2011-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian 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
11.93174.65499.40.06715.33.85514155141
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)
12.42.4799.90.4862.73.84518

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 4HSO2.419.5955115338499.250.19350.19140.2247RANDOM48.9273
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]
-1.57-0.052.18-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.116
r_dihedral_angle_4_deg17.425
r_dihedral_angle_3_deg15.357
r_dihedral_angle_1_deg4.962
r_mcangle_it2.248
r_angle_refined_deg1.444
r_mcbond_it1.397
r_mcbond_other1.395
r_angle_other_deg1.24
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.116
r_dihedral_angle_4_deg17.425
r_dihedral_angle_3_deg15.357
r_dihedral_angle_1_deg4.962
r_mcangle_it2.248
r_angle_refined_deg1.444
r_mcbond_it1.397
r_mcbond_other1.395
r_angle_other_deg1.24
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10404
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms39

Software

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