1Y1X

Structural analysis of a homolog of programmed cell death 6 protein from Leishmania major Friedlin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293Lithium sulfate, HEPES, magnesium sulfate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.651.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.754α = 90
b = 92.945β = 90
c = 52.137γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-30.97461SSRLBL11-3

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
11.875094.20.1248.85.73353133506-327.432
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)
11.871.9772.70.47322.73643

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPartial model from MAD experiments1.9546.472903829038157597.260.18980.18980.187450.23277RANDOM30.966
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]
0.01-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.795
r_dihedral_angle_4_deg16.675
r_dihedral_angle_3_deg13.002
r_scangle_it5.538
r_dihedral_angle_1_deg5.258
r_scbond_it4.217
r_mcangle_it3.59
r_mcbond_it2.726
r_angle_refined_deg1.392
r_angle_other_deg0.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.795
r_dihedral_angle_4_deg16.675
r_dihedral_angle_3_deg13.002
r_scangle_it5.538
r_dihedral_angle_1_deg5.258
r_scbond_it4.217
r_mcangle_it3.59
r_mcbond_it2.726
r_angle_refined_deg1.392
r_angle_other_deg0.852
r_mcbond_other0.827
r_nbd_refined0.222
r_nbtor_refined0.189
r_nbd_other0.17
r_symmetry_vdw_other0.167
r_xyhbond_nbd_refined0.152
r_metal_ion_refined0.132
r_symmetry_hbond_refined0.118
r_chiral_restr0.083
r_nbtor_other0.083
r_symmetry_vdw_refined0.053
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2827
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing