9Q86 | pdb_00009q86

McCP in complex with photocaged nitric oxide, 1.44 s, 9.5 microjoule, SSX


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE291Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4.
Crystal Properties
Matthews coefficientSolvent content
2.9558.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.183α = 90
b = 107.183β = 90
c = 107.183γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2021-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I241.00DiamondI24

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
1275.911000.9920.1225.86328000
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)
122.031000.3661.0420.748.8

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-VALUE275.9052800013321000.1630.16170.16170.19420.194237.22
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.751
r_dihedral_angle_3_deg14.138
r_lrange_it9.724
r_scangle_it8.889
r_dihedral_angle_2_deg7.006
r_dihedral_angle_1_deg6.906
r_scbond_it5.826
r_mcangle_it4.487
r_mcbond_it3.347
r_angle_refined_deg2.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.751
r_dihedral_angle_3_deg14.138
r_lrange_it9.724
r_scangle_it8.889
r_dihedral_angle_2_deg7.006
r_dihedral_angle_1_deg6.906
r_scbond_it5.826
r_mcangle_it4.487
r_mcbond_it3.347
r_angle_refined_deg2.494
r_nbtor_refined0.317
r_nbd_refined0.21
r_symmetry_nbd_refined0.201
r_xyhbond_nbd_refined0.141
r_chiral_restr0.122
r_symmetry_xyhbond_nbd_refined0.121
r_gen_planes_refined0.011
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2144
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms92

Software

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