5M9C | pdb_00005m9c

Human angiogenin ALS variant K40R


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ANG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52890.4 M Na/K tartrate 0.1 M Na citrate 20 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.1360.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.837α = 90
b = 116.074β = 90
c = 37.355γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
12.055895.40.998156.411150
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)
12.052.1169.60.8872.52.8616

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1ANG2.055810009113194.990.189090.184550.190.230570.24RANDOM37.191
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]
-2.25.74-3.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.86
r_dihedral_angle_3_deg15.769
r_dihedral_angle_4_deg14.787
r_long_range_B_refined7.603
r_long_range_B_other7.589
r_dihedral_angle_1_deg6.645
r_scangle_other4.717
r_mcangle_other3.823
r_mcangle_it3.82
r_scbond_it2.875
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms970
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing