2WN9

Crystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYNPDB ENTRY 2BYN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
126% PEG400, 0.1 M HEPES, PH 7.5, 0.2 M MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.909α = 90
b = 115.394β = 90
c = 130.607γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

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
11.7556.899.90.0520.76.513253724.1
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)
11.751.841000.394.56.4

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 2BYN1.7520125779658499.910.171310.169650.20308RANDOM32.431
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]
1.08-0.73-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_4_deg20.581
r_dihedral_angle_3_deg14.029
r_dihedral_angle_1_deg6.11
r_scangle_it4.548
r_scbond_it3.091
r_mcangle_it2.828
r_mcbond_it2.036
r_angle_refined_deg1.489
r_angle_other_deg0.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_4_deg20.581
r_dihedral_angle_3_deg14.029
r_dihedral_angle_1_deg6.11
r_scangle_it4.548
r_scbond_it3.091
r_mcangle_it2.828
r_mcbond_it2.036
r_angle_refined_deg1.489
r_angle_other_deg0.808
r_mcbond_other0.619
r_symmetry_vdw_other0.24
r_symmetry_hbond_refined0.232
r_nbd_other0.195
r_nbd_refined0.193
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.147
r_symmetry_vdw_refined0.091
r_chiral_restr0.09
r_nbtor_other0.086
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.003
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_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 Atoms8406
Nucleic Acid Atoms
Solvent Atoms780
Heterogen Atoms185

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing