9EWJ | pdb_00009ewj

Dye-decolourising peroxidase DtpB (224 kGy)


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.52936.2 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
2.5852.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.85α = 90
b = 121.896β = 90
c = 199.551γ = 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
1silicon chipfixed 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
121858

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
11.9240.111000.980.1241.8378.3161825
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)
11.921.9799.80.570.70512.5

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 REPLACEMENTTHROUGHOUT1.9240.11153678804499.970.20980.207990.21260.245090.246RANDOM33.594
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]
0.02-0.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.194
r_dihedral_angle_2_deg15.156
r_long_range_B_refined9.324
r_long_range_B_other9.323
r_scangle_other8.518
r_dihedral_angle_1_deg7.684
r_mcangle_it6.324
r_mcangle_other6.324
r_scbond_it5.958
r_scbond_other5.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.194
r_dihedral_angle_2_deg15.156
r_long_range_B_refined9.324
r_long_range_B_other9.323
r_scangle_other8.518
r_dihedral_angle_1_deg7.684
r_mcangle_it6.324
r_mcangle_other6.324
r_scbond_it5.958
r_scbond_other5.958
r_mcbond_it4.351
r_mcbond_other4.351
r_angle_refined_deg2.57
r_angle_other_deg0.89
r_chiral_restr0.113
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.006
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 Atoms13926
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms173

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing