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Crystal structure of CD84: Insite into SLAM family function
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 20% PEG3350, 0.3 M MgCl2, 0.1 M, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.013 α = 90 b = 170.982 β = 90 c = 148.527 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm X9A 2005-09-26 M MAD 2 1 x-ray 100 CCD ADSC QUANTUM 315 X29A 2005-09-26 M SINGLE WAVELENGTH 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 0.961, 0.9797, 0.9794 NSLS X9A 2 SYNCHROTRON NSLS BEAMLINE X29A 1.1 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 1.98 50 90.2 0.072 11.3 3.6 39739
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) 1.98 2.05 15.1 0.406 1.3 810
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.043 20 39654 1999 79.98 0.201 0.197 0.277 0.3009 RANDOM 44.174
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] -0.06 -0.02 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.466 r_dihedral_angle_4_deg 21.592 r_dihedral_angle_3_deg 18.91 r_dihedral_angle_1_deg 7.821 r_scangle_it 5.37 r_scbond_it 3.412 r_mcangle_it 2.68 r_angle_refined_deg 1.938 r_mcbond_it 1.56 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.466 r_dihedral_angle_4_deg 21.592 r_dihedral_angle_3_deg 18.91 r_dihedral_angle_1_deg 7.821 r_scangle_it 5.37 r_scbond_it 3.412 r_mcangle_it 2.68 r_angle_refined_deg 1.938 r_mcbond_it 1.56 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.234 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.136 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5243 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SHELXS phasing