1UN4

CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T80A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B1IPDB ENTRY 1B1I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.215% PEG 4000, 0.02% DIOXANE, 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER, PH 5.2
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.549α = 90
b = 38.297β = 90
c = 39.043γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC CCDRH/SI MIRROR2001-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
12.14098.60.05613.64.67942
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1897.30.2335.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B1I2.143.44755136798.60.1930.1910.232RANDOM28.81
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]
-0.96-0.831.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.959
r_scangle_it2.665
r_scbond_it1.652
r_mcangle_it1.411
r_angle_other_deg1.258
r_mcbond_it0.763
r_nbd_refined0.179
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_refined0.129
r_symmetry_hbond_refined0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.959
r_scangle_it2.665
r_scbond_it1.652
r_mcangle_it1.411
r_angle_other_deg1.258
r_mcbond_it0.763
r_nbd_refined0.179
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_refined0.129
r_symmetry_hbond_refined0.117
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_refined_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms913
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing