2BYN

Crystal structure of apo AChBP from Aplysia californica


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UX2PDB ENTRY 1UX2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.612-14% PEG 4000, 0.1 M SODIUM CITRATE, PH 5.6, 20% ISOPROPANOL, 5% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.855.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.153α = 90
b = 146.768β = 90
c = 143.307γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.025098.50.0613.66.297846

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 1UX22.0240.0394830298098.50.170.1690.202RANDOM38.51
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]
-1.362.49-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.033
r_dihedral_angle_4_deg23.07
r_dihedral_angle_3_deg14.505
r_dihedral_angle_1_deg6.736
r_scangle_it2.836
r_scbond_it1.884
r_angle_refined_deg1.411
r_mcangle_it1.357
r_mcbond_it0.905
r_angle_other_deg0.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.033
r_dihedral_angle_4_deg23.07
r_dihedral_angle_3_deg14.505
r_dihedral_angle_1_deg6.736
r_scangle_it2.836
r_scbond_it1.884
r_angle_refined_deg1.411
r_mcangle_it1.357
r_mcbond_it0.905
r_angle_other_deg0.779
r_symmetry_vdw_other0.275
r_symmetry_vdw_refined0.232
r_symmetry_hbond_refined0.214
r_nbd_other0.197
r_xyhbond_nbd_refined0.195
r_nbd_refined0.192
r_nbtor_refined0.175
r_nbtor_other0.084
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms8512
Nucleic Acid Atoms
Solvent Atoms882
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing