8Q6M | pdb_00008q6m

Human SOD1 low dose data collecton


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C9V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.752932.5 M Ammonium sulphate, Acetate buffer pH 4.75
Crystal Properties
Matthews coefficientSolvent content
2.110.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.26α = 90
b = 68.01β = 106.28
c = 52.58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2023-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.54180

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.7737.6997.30.1350.1840.1250.9743.93.325235
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.810.4110.5690.3930.6493.3

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-VALUE1.7735.3382522093397.2210.2110.20890.220.25050.2619.766
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]
0.994-1.423-1.2410.921
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.885
r_dihedral_angle_3_deg14.812
r_dihedral_angle_4_deg14.336
r_dihedral_angle_1_deg9.904
r_lrange_it5.173
r_lrange_other4.815
r_scangle_it3.067
r_scangle_other3.031
r_mcangle_it2.4
r_mcangle_other2.4
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2220
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing