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The crystal structure of natural killer cell receptor Ly49C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4L PDB ENTRY 1P4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 2.0 M ammonium sulfate, 2% (volume/volume) PEG 400 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.77 30.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.097 α = 90 b = 94.892 β = 90 c = 104.192 γ = 90
Symmetry Space Group P 21 21 21
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 2004-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 96.4 0.058 30.8 6.2 21005 48.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 97.4 0.357 3.56 4.8 2076
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 (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 PDB ENTRY 1P4L 2.6 30 19233 1039 93.48 0.20157 0.19832 0.2588 0.26322 0.3051 RANDOM 60.139
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] 2.66 -1.32 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.565 r_dihedral_angle_4_deg 21.169 r_dihedral_angle_3_deg 19.201 r_dihedral_angle_1_deg 7.318 r_scangle_it 1.954 r_angle_refined_deg 1.427 r_scbond_it 1.26 r_mcangle_it 0.951 r_mcbond_it 0.544 r_symmetry_hbond_refined 0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.565 r_dihedral_angle_4_deg 21.169 r_dihedral_angle_3_deg 19.201 r_dihedral_angle_1_deg 7.318 r_scangle_it 1.954 r_angle_refined_deg 1.427 r_scbond_it 1.26 r_mcangle_it 0.951 r_mcbond_it 0.544 r_symmetry_hbond_refined 0.409 r_symmetry_vdw_refined 0.356 r_nbtor_refined 0.319 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4236 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing