5PY8

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 68)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.1M MES pH 6.1 -- 20% PEG20K
Crystal Properties
Matthews coefficientSolvent content
2.7455.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.71α = 90
b = 45.3β = 102.26
c = 83.38γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-04-02SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6638.9195.50.1020.1220.0660.99311.93.352741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.797.40.60.7120.3790.7823.53942

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4PTB1.6638.9150102263895.070.20890.20670.2518RANDOM30.302
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]
-1.94-0.041.520.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.491
r_dihedral_angle_4_deg15.44
r_dihedral_angle_3_deg13.548
r_dihedral_angle_1_deg6.562
r_mcangle_it5.258
r_mcbond_it3.282
r_mcbond_other3.282
r_angle_refined_deg1.908
r_angle_other_deg1.093
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.491
r_dihedral_angle_4_deg15.44
r_dihedral_angle_3_deg13.548
r_dihedral_angle_1_deg6.562
r_mcangle_it5.258
r_mcbond_it3.282
r_mcbond_other3.282
r_angle_refined_deg1.908
r_angle_other_deg1.093
r_chiral_restr0.126
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2925
Nucleic Acid Atoms
Solvent Atoms579
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing