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NKR-P1B from Rattus norvegicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 80 mM HEPES, pH 7.5, 20% (w/v) PEG3000, 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.721 α = 90 b = 60.721 β = 90 c = 76.589 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 MARMOSAIC 225 mm CCD 2011-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 52.59 100 0.078 21.8 3.3 21405 40
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 2 2.04 100 0.702 2.1 3.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2YHF 2 52.59 21380 677 99.79 0.22134 0.22134 0.2267 0.262 random selection 54.708
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] -0.66 -0.33 -0.66 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 25.076 r_dihedral_angle_3_deg 15.522 r_long_range_B_refined 9.627 r_long_range_B_other 9.593 r_dihedral_angle_1_deg 8.901 r_scangle_other 7.258 r_mcangle_it 6.629 r_mcangle_other 6.628 r_scbond_it 4.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 25.076 r_dihedral_angle_3_deg 15.522 r_long_range_B_refined 9.627 r_long_range_B_other 9.593 r_dihedral_angle_1_deg 8.901 r_scangle_other 7.258 r_mcangle_it 6.629 r_mcangle_other 6.628 r_scbond_it 4.626 r_scbond_other 4.624 r_mcbond_it 4.575 r_mcbond_other 4.569 r_angle_refined_deg 1.813 r_angle_other_deg 1.043 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing