9HL1 | pdb_00009hl1

DtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoule, SFX


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29150 mM HEPES pH 7.5, 150 mM Magnesium chloride, 20% (w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6353.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.073α = 90
b = 122.875β = 90
c = 194.936γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300CCDRAYONIX MX-3002023-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.127SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
110 (fs)3000010.993 (KeV)

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
11.56103.951000.9940.09618.1168.6295889
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)
11.561.590.3161.2560.9

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 REPLACEMENTTHROUGHOUT1.5644.68293539202799.890.208910.208740.21950.233630.2437RANDOM23.355
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]
-0.290.140.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.268
r_dihedral_angle_2_deg8.51
r_long_range_B_refined7.509
r_long_range_B_other7.468
r_dihedral_angle_1_deg6.431
r_scangle_other5.945
r_scbond_it3.848
r_scbond_other3.837
r_mcangle_it3.545
r_mcangle_other3.545
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.268
r_dihedral_angle_2_deg8.51
r_long_range_B_refined7.509
r_long_range_B_other7.468
r_dihedral_angle_1_deg6.431
r_scangle_other5.945
r_scbond_it3.848
r_scbond_other3.837
r_mcangle_it3.545
r_mcangle_other3.545
r_mcbond_it2.418
r_mcbond_other2.417
r_angle_refined_deg1.98
r_angle_other_deg0.703
r_chiral_restr0.104
r_bond_refined_d0.012
r_gen_planes_refined0.01
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 Atoms13944
Nucleic Acid Atoms
Solvent Atoms1102
Heterogen Atoms270

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing