4RC7

Crystal structure of cyanobacterial aldehyde-deformylating oxygenase F86YF87Y mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12910.02M adenosine-5'-triphosphate disodium salt hydrate, 0.2M L-proline, 0.1M Hepes pH 7.1, 25%(w/v) PEG1500 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3848.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.014α = 90
b = 62.109β = 90
c = 125.003γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.7382SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.25098.52508924713
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2899.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4QUW2.241.4072381523389125298.210.206760.205140.23763RANDOM26.482
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]
-0.56-0.410.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.297
r_dihedral_angle_4_deg21.294
r_dihedral_angle_3_deg15.961
r_long_range_B_refined5.074
r_long_range_B_other5.062
r_dihedral_angle_1_deg4.301
r_scangle_other3.922
r_angle_other_deg3.604
r_scbond_other2.677
r_scbond_it2.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.297
r_dihedral_angle_4_deg21.294
r_dihedral_angle_3_deg15.961
r_long_range_B_refined5.074
r_long_range_B_other5.062
r_dihedral_angle_1_deg4.301
r_scangle_other3.922
r_angle_other_deg3.604
r_scbond_other2.677
r_scbond_it2.481
r_mcangle_it2.048
r_mcangle_other2.047
r_mcbond_it1.353
r_mcbond_other1.353
r_angle_refined_deg1.145
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_other0.006
r_gen_planes_refined0.004
r_bond_other_d
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 Atoms3549
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms38

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling