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Structure of the peptidylprolyl isomerase domain of the human NK-tumour recognition protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZCX pdb entry 1ZCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Well solution: 21% Peg 3350, 0.25M potassium sulfate; Protein solution: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 15 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.753 α = 90 b = 72.786 β = 90 c = 73.014 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2006-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 99.9 0.146 15.2 7 23807 23807 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 98.7 0.769 6.5 2317
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 (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 1ZCX 2 19.91 23772 22557 1215 99.9 0.14889 0.14631 0.1548 0.19752 0.2017 RANDOM 20.605
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] -0.82 1.59 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 12.663 r_dihedral_angle_1_deg 6.306 r_scangle_it 5.543 r_scbond_it 4.025 r_mcangle_it 2.503 r_mcbond_it 2.12 r_angle_refined_deg 1.515 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 12.663 r_dihedral_angle_1_deg 6.306 r_scangle_it 5.543 r_scbond_it 4.025 r_mcangle_it 2.503 r_mcbond_it 2.12 r_angle_refined_deg 1.515 r_nbtor_refined 0.315 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2708 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PHASER phasing