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Structural analysis of a homolog of programmed cell death 6 protein from Leishmania major Friedlin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Partial model from MAD experiments
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Lithium sulfate, HEPES, magnesium sulfate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.754 α = 90 b = 92.945 β = 90 c = 52.137 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2004-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-3 0.97461 SSRL BL11-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.87 50 94.2 0.124 8.8 5.7 33531 33506 -3 27.432
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97 72.7 0.473 2 2.7 3643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Partial model from MAD experiments 1.95 46.47 29038 29038 1575 97.26 0.1898 0.1898 0.18745 0.1974 0.23277 0.2419 RANDOM 30.966
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 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.795 r_dihedral_angle_4_deg 16.675 r_dihedral_angle_3_deg 13.002 r_scangle_it 5.538 r_dihedral_angle_1_deg 5.258 r_scbond_it 4.217 r_mcangle_it 3.59 r_mcbond_it 2.726 r_angle_refined_deg 1.392 r_angle_other_deg 0.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.795 r_dihedral_angle_4_deg 16.675 r_dihedral_angle_3_deg 13.002 r_scangle_it 5.538 r_dihedral_angle_1_deg 5.258 r_scbond_it 4.217 r_mcangle_it 3.59 r_mcbond_it 2.726 r_angle_refined_deg 1.392 r_angle_other_deg 0.852 r_mcbond_other 0.827 r_nbd_refined 0.222 r_nbtor_refined 0.189 r_nbd_other 0.17 r_symmetry_vdw_other 0.167 r_xyhbond_nbd_refined 0.152 r_metal_ion_refined 0.132 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.083 r_nbtor_other 0.083 r_symmetry_vdw_refined 0.053 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2827 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing