5Z54

Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239 in complex with cyclo-L-Arg-D-Pro


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YVK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82950.2M sodium chloride, 20%(w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3647.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.557α = 90
b = 113.374β = 90
c = 132.332γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.162599.80.0880.0910.0247.214.349997
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)
12.282.3698.20.4950.5170.1460.95511.6

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 REPLACEMENTTHROUGHOUT5YVK2.1624.947439249396.840.184060.181620.23028RANDOM48.001
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]
-4.985.7-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.224
r_dihedral_angle_4_deg19.228
r_dihedral_angle_3_deg17.352
r_long_range_B_refined9.939
r_dihedral_angle_1_deg8.157
r_scbond_it5.414
r_mcangle_it5.19
r_mcbond_it3.765
r_angle_refined_deg1.452
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.224
r_dihedral_angle_4_deg19.228
r_dihedral_angle_3_deg17.352
r_long_range_B_refined9.939
r_dihedral_angle_1_deg8.157
r_scbond_it5.414
r_mcangle_it5.19
r_mcbond_it3.765
r_angle_refined_deg1.452
r_chiral_restr0.106
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6144
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing