7YKB | pdb_00007ykb

Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin at Room Temperature


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F0M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293NaCl, ammonium sulfate, MES
Crystal Properties
Matthews coefficientSolvent content
2.7455.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.174α = 90
b = 97.523β = 90
c = 43.277γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300PIXELDECTRIS PILATUS3 2M2021-06-06MSINGLE WAVELENGTH
21neutron300DIFFRACTOMETERiBIX2021-03-20LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A
2SPALLATION SOURCEJ-PARC MLF BEAMLINE BL-032.63-6.06JPARC MLFBL-03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (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
11.3843.2899.60.99712.24.96240215.07
22.121.1699.30.98289.186.93771815815.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.40.752
22.12.170.4789

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.3834.581.3562359112799.340.15050.15010.150.17160.1717.93
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.121.121815898.68470.16570.1806
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
f_dihedral_angle_d19.4914
f_angle_d1.4608
f_chiral_restr0.0921
f_bond_d0.016
f_plane_restr0.0117
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1925
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms44

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACphasing