1K5B

Crystal Structure of Human Angiogenin Variant des(121-123)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ANGPDB ENTRY 2ANG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2289sodium citrate, sodium potassium tartrate, PEG 6000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.141.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.45α = 90
b = 40.41β = 90
c = 32.98γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293AREA DETECTORXENTRONICS1997-02-11MSINGLE WAVELENGTH
21x-ray293IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODESIEMENS1.5418
2SYNCHROTRONSRS BEAMLINE PX9.50.8SRSPX9.5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1,21.83092.30.07311.73.81015810158-3-321.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.990

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ANG1.8209945994552888.40.2060.2060.2060.275RANDOM29.9
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
x_dihedral_angle_d27.5
x_scangle_it5.6
x_scbond_it3.75
x_mcangle_it3.61
x_mcbond_it2.28
x_angle_deg1.8
x_improper_angle_d0.81
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d27.5
x_scangle_it5.6
x_scbond_it3.75
x_mcangle_it3.61
x_mcbond_it2.28
x_angle_deg1.8
x_improper_angle_d0.81
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms967
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms13

Software

Software
Software NamePurpose
X-GENdata scaling
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
X-GENdata reduction