1VKB | pdb_00001vkb

Crystal structure of an aig2-like protein (a2ld1, ggact, mgc7867) from mus musculus at 1.90 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP2934.1 Acetate, 2.4 NaFormate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.745α = 90
b = 85.745β = 90
c = 42.858γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2003-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.95099.960.04886.2160.451436426.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9799.930.12227.430.782772

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.942.871362572099.990.136090.134160.150.170580.18RANDOM18.317
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]
0.150.070.15-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.633
r_dihedral_angle_4_deg13.45
r_dihedral_angle_3_deg11.468
r_scangle_it6.652
r_dihedral_angle_1_deg6.264
r_scbond_it4.95
r_mcangle_it3.168
r_mcbond_it2.227
r_angle_refined_deg1.605
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.633
r_dihedral_angle_4_deg13.45
r_dihedral_angle_3_deg11.468
r_scangle_it6.652
r_dihedral_angle_1_deg6.264
r_scbond_it4.95
r_mcangle_it3.168
r_mcbond_it2.227
r_angle_refined_deg1.605
r_angle_other_deg0.941
r_mcbond_other0.634
r_symmetry_hbond_refined0.259
r_symmetry_vdw_other0.237
r_nbd_refined0.199
r_nbd_other0.19
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.156
r_chiral_restr0.109
r_nbtor_other0.084
r_bond_refined_d0.015
r_bond_other_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1188
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms9

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
autoSHARPphasing
SOLOMONphasing
REFMACrefinement
SHELXphasing