2GXS | pdb_00002gxs

HERA N-terminal domain in complex with AMP, crystal form 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP929514% PEG6000, 0.3M CaCl2, 0.1M Tris/HCl pH9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2144.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.564α = 90
b = 42.838β = 100.06
c = 68.645γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray140IMAGE PLATEMAR scanner 345 mm plateosmic mirrors2006-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5419

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
11.665097.60.04827.54.1455114551127.6
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)
11.661.7285.60.51.93.13976

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.665043198230297.630.191720.189190.20.239420.24RANDOM20.853
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]
1.21-0.39-0.16-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.433
r_dihedral_angle_4_deg18.286
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg5.269
r_scangle_it3.865
r_scbond_it2.511
r_angle_refined_deg1.71
r_mcangle_it1.632
r_mcbond_it1.119
r_angle_other_deg1.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.433
r_dihedral_angle_4_deg18.286
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg5.269
r_scangle_it3.865
r_scbond_it2.511
r_angle_refined_deg1.71
r_mcangle_it1.632
r_mcbond_it1.119
r_angle_other_deg1.058
r_symmetry_vdw_refined0.292
r_symmetry_vdw_other0.262
r_mcbond_other0.252
r_nbd_refined0.232
r_nbd_other0.216
r_metal_ion_refined0.195
r_xyhbond_nbd_refined0.18
r_nbtor_refined0.174
r_symmetry_hbond_refined0.157
r_chiral_restr0.094
r_nbtor_other0.082
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3132
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data scaling
COMOphasing