4N59

The Crystal Structure of Pectocin M2 at 2.3 Angstroms


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529315 % PEG3350, 0.2 M Ammonium sulphate, 3% MPD, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5551.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.649α = 90
b = 116.745β = 94.96
c = 60.79γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

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
12.35096.60.0512.413.255667526522
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)
12.32.4495.70.5991.852.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTpdb entry 4N582.344.522625026116138499.490.209640.206340.27369RANDOM67.992
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]
-0.08-0.59-1.41.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.071
r_dihedral_angle_3_deg17.141
r_dihedral_angle_4_deg13.398
r_long_range_B_refined8.263
r_long_range_B_other8.254
r_dihedral_angle_1_deg6.752
r_scangle_other4.687
r_mcangle_other4.374
r_mcangle_it4.12
r_scbond_it3.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.071
r_dihedral_angle_3_deg17.141
r_dihedral_angle_4_deg13.398
r_long_range_B_refined8.263
r_long_range_B_other8.254
r_dihedral_angle_1_deg6.752
r_scangle_other4.687
r_mcangle_other4.374
r_mcangle_it4.12
r_scbond_it3.053
r_scbond_other2.944
r_mcbond_it2.461
r_mcbond_other2.457
r_angle_refined_deg1.7
r_angle_other_deg0.866
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms4079
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms34

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction