9FBC | pdb_00009fbc

Dye-decolourising peroxidase DtpB (448 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
2.6252.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.984α = 90
b = 121.963β = 90
c = 199.607γ = 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
116846

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
12.7240.161000.99250.1151.2140.557840
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)
12.722.790.520.7820.47

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 REPLACEMENTTHROUGHOUT2.7240.1654838293199.930.237530.234960.23380.286250.2801RANDOM56.912
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]
0.11-0.330.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.676
r_long_range_B_refined14.687
r_long_range_B_other14.686
r_dihedral_angle_2_deg12.672
r_scangle_other12.453
r_mcangle_it11.552
r_mcangle_other11.551
r_dihedral_angle_1_deg8.995
r_scbond_it8.602
r_scbond_other8.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.676
r_long_range_B_refined14.687
r_long_range_B_other14.686
r_dihedral_angle_2_deg12.672
r_scangle_other12.453
r_mcangle_it11.552
r_mcangle_other11.551
r_dihedral_angle_1_deg8.995
r_scbond_it8.602
r_scbond_other8.602
r_mcbond_it7.97
r_mcbond_other7.97
r_angle_refined_deg2.692
r_angle_other_deg0.883
r_chiral_restr0.112
r_bond_refined_d0.014
r_gen_planes_refined0.01
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 Atoms13766
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing