6Z3C | pdb_00006z3c

High resolution structure of RgNanOx


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Z3B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG3000, sodium citrate,
Crystal Properties
Matthews coefficientSolvent content
2.1843.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.11α = 90
b = 54.97β = 90
c = 282.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2019-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.7447.4710015.66.393221
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)
11.741.770.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE6Z3B1.7447.4778180383199.8190.1840.18210.20.22260.2317.448
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]
0.996-0.985-0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.245
r_dihedral_angle_4_deg23.814
r_dihedral_angle_3_deg12.866
r_lrange_it9.087
r_lrange_other9.062
r_scangle_it8.278
r_scangle_other8.277
r_dihedral_angle_1_deg7.074
r_scbond_other6.817
r_scbond_it6.816
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5919
Nucleic Acid Atoms
Solvent Atoms850
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
XSCALEdata scaling
PHASERphasing