9HTC | pdb_00009htc

McCP in complex with photocaged nitric oxide, 1.44 s, 1600 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
2.9563.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.441α = 90
b = 107.441β = 90
c = 107.441γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2019-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.969DiamondI24

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Oxford silicon chipfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlDetails Sample Solvent
1Geobrick 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
11.876.091000.9860.0710.2159.838525
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)
11.81.831000.2911.2340.7127.2

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-VALUE1.876.093852320381000.1620.16050.16480.19460.198635.534
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_deg15.525
r_dihedral_angle_3_deg12.237
r_dihedral_angle_1_deg10.561
r_lrange_it10.187
r_scangle_it8.971
r_scbond_it5.953
r_dihedral_angle_2_deg5.645
r_mcangle_it4.6
r_mcbond_it3.53
r_angle_refined_deg2.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.525
r_dihedral_angle_3_deg12.237
r_dihedral_angle_1_deg10.561
r_lrange_it10.187
r_scangle_it8.971
r_scbond_it5.953
r_dihedral_angle_2_deg5.645
r_mcangle_it4.6
r_mcbond_it3.53
r_angle_refined_deg2.514
r_nbtor_refined0.313
r_metal_ion_refined0.28
r_nbd_refined0.206
r_symmetry_nbd_refined0.176
r_chiral_restr0.131
r_xyhbond_nbd_refined0.108
r_symmetry_xyhbond_nbd_refined0.06
r_gen_planes_refined0.013
r_bond_refined_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2144
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms104

Software

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