9HXX | pdb_00009hxx

DtpB in complex with photocaged nitric oxide, 100 microsecond, 30 microjoule, SFX


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29350 mM HEPES pH 7.5, 150 mM Magnesium chloride 20% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6453.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.475α = 90
b = 124.392β = 90
c = 193.508γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDRAYONIX MX300-HS2023-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.127SACLABL2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.52104.641000.99619.4167322685
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.551000.317

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 REPLACEMENTTHROUGHOUT1.5245.13320258208499.890.209160.208990.21980.23530.245RANDOM22.938
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]
-0.150.140.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.397
r_dihedral_angle_2_deg8.084
r_long_range_B_refined7.599
r_long_range_B_other7.561
r_dihedral_angle_1_deg7.215
r_scangle_other5.902
r_scbond_it3.845
r_scbond_other3.832
r_mcangle_it3.499
r_mcangle_other3.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.397
r_dihedral_angle_2_deg8.084
r_long_range_B_refined7.599
r_long_range_B_other7.561
r_dihedral_angle_1_deg7.215
r_scangle_other5.902
r_scbond_it3.845
r_scbond_other3.832
r_mcangle_it3.499
r_mcangle_other3.499
r_mcbond_it2.351
r_mcbond_other2.351
r_angle_refined_deg1.954
r_angle_other_deg0.683
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
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 Atoms1078
Heterogen Atoms278

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
xia2data reduction
PHASERphasing