6MUK

1.93 Angstrom Resolution Crystal Structure of Peptidase M23 from Neisseria gonorrhoeae.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292Protein: 13.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (C2), 1.1M Ammonium tartrate pH 7.0; Cryo: 4M Sodium formate.
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.964α = 90
b = 66.964β = 90
c = 181.584γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.93301000.0490.0490.0530.0238.77.232097-336.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.961000.8410.8410.9040.330.8642.57.3

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 REPLACEMENTTHROUGHOUT3SLU1.9329.9530417160699.950.190790.188490.23554RANDOM44.127
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]
1.521.52-3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.818
r_dihedral_angle_4_deg12.608
r_dihedral_angle_3_deg11.056
r_long_range_B_refined7.113
r_long_range_B_other7.098
r_dihedral_angle_1_deg3.78
r_scangle_other3.566
r_mcangle_it2.887
r_mcangle_other2.887
r_scbond_it2.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.818
r_dihedral_angle_4_deg12.608
r_dihedral_angle_3_deg11.056
r_long_range_B_refined7.113
r_long_range_B_other7.098
r_dihedral_angle_1_deg3.78
r_scangle_other3.566
r_mcangle_it2.887
r_mcangle_other2.887
r_scbond_it2.239
r_scbond_other2.235
r_mcbond_it1.863
r_mcbond_other1.859
r_angle_refined_deg1.388
r_angle_other_deg0.408
r_chiral_restr0.056
r_gen_planes_refined0.053
r_gen_planes_other0.047
r_bond_refined_d0.008
r_bond_other_d0.001
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 Atoms2760
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing