7PZH

Phocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6NJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529312.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulphate, 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.244.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.233α = 90
b = 93.233β = 90
c = 353.623γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97624DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0680.741000.99811.220.5106903
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.10.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6njc2.0680.742106769535599.9880.1870.1850.225837.958
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]
-0.037-0.0370.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.977
r_dihedral_angle_4_deg16.72
r_dihedral_angle_3_deg16.037
r_dihedral_angle_1_deg7.614
r_lrange_it6.546
r_lrange_other6.546
r_scangle_it5.054
r_scangle_other5.051
r_mcangle_it4.566
r_mcangle_other4.566
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.977
r_dihedral_angle_4_deg16.72
r_dihedral_angle_3_deg16.037
r_dihedral_angle_1_deg7.614
r_lrange_it6.546
r_lrange_other6.546
r_scangle_it5.054
r_scangle_other5.051
r_mcangle_it4.566
r_mcangle_other4.566
r_scbond_it3.606
r_scbond_other3.602
r_mcbond_it3.517
r_mcbond_other3.517
r_angle_refined_deg1.646
r_angle_other_deg1.32
r_nbd_refined0.218
r_nbd_other0.209
r_symmetry_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.198
r_symmetry_nbd_other0.196
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.099
r_symmetry_nbtor_other0.083
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12619
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing