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Crystal structure of human CD59
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 294 0.1 M sodium citrate, 16 % polyethylene glycol 6000, 5% isopropanol, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.06 40.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.4 α = 90 b = 56.4 β = 90 c = 39.4 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 MAR CCD 225 mm 2005-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.75 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.12 28.2 99.3 0.051 0.051 52.9 12.2 4118 4118 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.2 93 0.141 0.141 12.5 10.9 386
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 1CDQ 2.12 28.2 4115 4115 189 99.28 0.18 0.18 0.177 0.1725 0.254 0.2567 RANDOM 22.672
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] -0.95 -0.48 -0.95 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.237 r_dihedral_angle_4_deg 16.183 r_dihedral_angle_3_deg 15.533 r_dihedral_angle_1_deg 7.224 r_scangle_it 2.77 r_scbond_it 1.694 r_angle_refined_deg 1.44 r_mcangle_it 0.996 r_mcbond_it 0.505 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.237 r_dihedral_angle_4_deg 16.183 r_dihedral_angle_3_deg 15.533 r_dihedral_angle_1_deg 7.224 r_scangle_it 2.77 r_scbond_it 1.694 r_angle_refined_deg 1.44 r_mcangle_it 0.996 r_mcbond_it 0.505 r_nbtor_refined 0.3 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.205 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 608 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing