9LUZ | pdb_00009luz

Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NPE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293.15Tris pH 7.5, (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
6.3180.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 210.242α = 90
b = 210.242β = 90
c = 210.242γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98.15PIXELDECTRIS EIGER X 16M2021-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95365Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.348.399.980.99917.53.670655
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.351001.20.429

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.348.27970551314399.9770.1920.19110.19110.20930.2093RANDOM47.863
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.798
r_dihedral_angle_6_deg17.71
r_dihedral_angle_1_deg7.094
r_lrange_it6.557
r_lrange_other6.557
r_scangle_other5.688
r_scangle_it5.636
r_scbond_it3.965
r_scbond_other3.964
r_dihedral_angle_2_deg3.891
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.798
r_dihedral_angle_6_deg17.71
r_dihedral_angle_1_deg7.094
r_lrange_it6.557
r_lrange_other6.557
r_scangle_other5.688
r_scangle_it5.636
r_scbond_it3.965
r_scbond_other3.964
r_dihedral_angle_2_deg3.891
r_mcangle_it3.769
r_mcangle_other3.768
r_mcbond_it2.405
r_mcbond_other2.405
r_angle_refined_deg1.447
r_angle_other_deg0.745
r_symmetry_nbd_other0.221
r_nbd_refined0.207
r_nbd_other0.198
r_nbtor_refined0.185
r_symmetry_xyhbond_nbd_refined0.151
r_xyhbond_nbd_refined0.133
r_symmetry_nbd_refined0.125
r_symmetry_nbtor_other0.092
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4261
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing