3MK4

X-Ray structure of human PEX3 in complex with a PEX19 derived peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherunrefined model of PEX3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629324% PEG 3350, 0.1M Bis-Tris, 0.2M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9537

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.47α = 90
b = 65.67β = 91.53
c = 61.58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2009-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
12.422599.70.10820.23.7117793
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)
12.422.4899.80.6833.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTunrefined model of PEX32.4224.9712726111905891000.196340.194310.23368RANDOM17.488
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]
1.871.770.66-2.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.677
r_dihedral_angle_4_deg20.513
r_dihedral_angle_3_deg14.872
r_dihedral_angle_1_deg5.091
r_scangle_it4.236
r_scbond_it2.994
r_mcangle_it2.222
r_mcbond_it1.344
r_angle_refined_deg1.081
r_angle_other_deg0.853
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.677
r_dihedral_angle_4_deg20.513
r_dihedral_angle_3_deg14.872
r_dihedral_angle_1_deg5.091
r_scangle_it4.236
r_scbond_it2.994
r_mcangle_it2.222
r_mcbond_it1.344
r_angle_refined_deg1.081
r_angle_other_deg0.853
r_mcbond_other0.479
r_chiral_restr0.057
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2363
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling