9I6G | pdb_00009i6g

DtpB in complex with photocaged nitric oxide, 1.24 s, 16.1 microjoule, SSX


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2916-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5.
Crystal Properties
Matthews coefficientSolvent content
2.4549.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.142α = 90
b = 123.022β = 90
c = 195.394γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2023-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I241.000DiamondI24

Serial Crystallography

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

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
12.479.7131000.9580.23437.723.382830
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)
12.42.441000.3111.1571.417.4

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)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.479.71382830418499.9760.1940.19260.19320.21190.212137.763
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]
-1.1230.6980.425
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.633
r_dihedral_angle_6_deg11.733
r_dihedral_angle_1_deg5.647
r_lrange_it4.838
r_dihedral_angle_2_deg4.313
r_scangle_it2.895
r_mcangle_it2.477
r_scbond_it1.659
r_mcbond_it1.373
r_angle_refined_deg1.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.633
r_dihedral_angle_6_deg11.733
r_dihedral_angle_1_deg5.647
r_lrange_it4.838
r_dihedral_angle_2_deg4.313
r_scangle_it2.895
r_mcangle_it2.477
r_scbond_it1.659
r_mcbond_it1.373
r_angle_refined_deg1.065
r_nbtor_refined0.294
r_symmetry_nbd_refined0.246
r_symmetry_xyhbond_nbd_refined0.216
r_nbd_refined0.173
r_xyhbond_nbd_refined0.107
r_chiral_restr0.083
r_ncsr_local_group_50.08
r_ncsr_local_group_30.077
r_ncsr_local_group_140.076
r_ncsr_local_group_90.075
r_ncsr_local_group_10.073
r_ncsr_local_group_70.072
r_ncsr_local_group_120.072
r_ncsr_local_group_150.072
r_ncsr_local_group_20.07
r_ncsr_local_group_100.069
r_ncsr_local_group_40.067
r_ncsr_local_group_130.067
r_ncsr_local_group_60.066
r_ncsr_local_group_80.062
r_ncsr_local_group_110.062
r_bond_refined_d0.003
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13975
Nucleic Acid Atoms
Solvent Atoms538
Heterogen Atoms270

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Cootmodel building