5J5L

CRYSTAL STRUCTURE OF AFMP4P IN COMPLEX WITH ARACHIDONIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JOW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES PH 6.5, 25% POLYETHYLENE GLYCOL 4000, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.374α = 90
b = 124.374β = 90
c = 124.374γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97922SSRFBL17U

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
11.75099.70.063122318323
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)
11.71.761000.45723

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 REPLACEMENTTHROUGHOUT4JOW1.744.011831893899.60.1650.1630.19RANDOM28.37
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_3_deg10.649
r_dihedral_angle_1_deg3.965
r_mcangle_it1.692
r_mcbond_it1.375
r_mcbond_other1.287
r_angle_refined_deg1.077
r_angle_other_deg0.75
r_chiral_restr0.052
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_3_deg10.649
r_dihedral_angle_1_deg3.965
r_mcangle_it1.692
r_mcbond_it1.375
r_mcbond_other1.287
r_angle_refined_deg1.077
r_angle_other_deg0.75
r_chiral_restr0.052
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms1082
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms22

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement