9FBA | pdb_00009fba

Dye-decolourising peroxidase DtpB (392 kGy)


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YRJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2936.2 mg/mL of protein in 20 mM NaPi, 150 mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 18% PEG 4000 pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5952.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.965α = 90
b = 121.963β = 90
c = 199.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M2019-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlDetails Sample Solvent
1silicone chip
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1undefined (fs)undefined (KeV)
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
118590

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.440.151000.99040.1261.24113.383736
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.460.460.9270.39

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.440.1579480417899.930.243630.242070.24240.273110.2707RANDOM46.233
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]
0.01-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.962
r_dihedral_angle_2_deg10.901
r_long_range_B_refined10.779
r_long_range_B_other10.779
r_scangle_other8.588
r_dihedral_angle_1_deg8.014
r_mcangle_it7.724
r_mcangle_other7.724
r_scbond_other5.631
r_scbond_it5.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.962
r_dihedral_angle_2_deg10.901
r_long_range_B_refined10.779
r_long_range_B_other10.779
r_scangle_other8.588
r_dihedral_angle_1_deg8.014
r_mcangle_it7.724
r_mcangle_other7.724
r_scbond_other5.631
r_scbond_it5.63
r_mcbond_it5.084
r_mcbond_other5.084
r_angle_refined_deg2.103
r_angle_other_deg0.717
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms13934
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing