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Leishmania major Programmed Cell Death Protein 5 Homolog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 300 1.5 M K2HPO4
Crystal Properties Matthews coefficient Solvent content 2.82 56.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.386 α = 90 b = 115.386 β = 90 c = 58.628 γ = 120
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 315 2005-03-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.95373,0.97962,0.97949 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 25.296 87.8 0.114 0.122 0.04 0.998 11.3 8.9 4643
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 53.5 6.236 6.752 2.424 0.264 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6IQO 2.501 25.296 4640 194 87.829 0.224 0.2223 0.2175 0.2727 0.2755 79.593
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] -0.435 -0.218 -0.435 1.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.103 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 20.702 r_lrange_it 17.389 r_lrange_other 17.382 r_scangle_it 14.901 r_scangle_other 14.887 r_mcangle_it 9.843 r_mcangle_other 9.834 r_scbond_it 9.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.103 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 20.702 r_lrange_it 17.389 r_lrange_other 17.382 r_scangle_it 14.901 r_scangle_other 14.887 r_mcangle_it 9.843 r_mcangle_other 9.834 r_scbond_it 9.396 r_scbond_other 9.385 r_mcbond_it 7.567 r_mcbond_other 7.344 r_dihedral_angle_1_deg 5.778 r_angle_refined_deg 1.605 r_angle_other_deg 1.262 r_symmetry_nbd_refined 0.258 r_nbd_other 0.227 r_nbd_refined 0.222 r_symmetry_nbd_other 0.19 r_xyhbond_nbd_refined 0.154 r_nbtor_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 783 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MoRDa phasing