6A8X

Crystal structure of a apo form cyclase from Fischerella sp.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82951.0M sodium citrate, 0.1M Imidazole pH 8.0
Crystal Properties
Matthews coefficientSolvent content
5.0175.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.993α = 90
b = 90.993β = 90
c = 234.496γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002018-01-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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
12.352596.80.0770.0820.02812.28.940767
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)
12.352.431000.7060.7450.2310.85610.1

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 REPLACEMENTTHROUGHOUT5YVK2.3524.8538471195996.170.196920.195060.2334RANDOM54.156
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]
-0.89-0.891.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.126
r_dihedral_angle_4_deg20.35
r_dihedral_angle_3_deg18.328
r_long_range_B_other10.256
r_long_range_B_refined10.245
r_scangle_other8.911
r_dihedral_angle_1_deg7.983
r_scbond_it6.644
r_scbond_other6.642
r_mcangle_it6.539
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.126
r_dihedral_angle_4_deg20.35
r_dihedral_angle_3_deg18.328
r_long_range_B_other10.256
r_long_range_B_refined10.245
r_scangle_other8.911
r_dihedral_angle_1_deg7.983
r_scbond_it6.644
r_scbond_other6.642
r_mcangle_it6.539
r_mcangle_other6.538
r_mcbond_it5.073
r_mcbond_other5.056
r_angle_refined_deg1.38
r_angle_other_deg0.86
r_chiral_restr0.063
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms3088
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms4

Software

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