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Structure of the Cyclophilin_CeCYP16-Like Domain of the Serologically Defined Colon Cancer Antigen 10 from Homo Sapiens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZKC pdb entry 1ZKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 Protein is 20 mg/mL, in buffer containing 50 mM Tris pH 8.0, 500 mM NaCl, 5 mM BME; hanging drop, 1+1; precipitant is 20% Peg 3350, 0.2M NaI (no buffer); cryo was 20% glycerol, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.433 α = 90 b = 84.433 β = 90 c = 55.289 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 IMAGE PLATE RIGAKU RAXIS IV 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 1.75 24.7 98.5 0.136 9.2 3.2 22463 22463 -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) 1 1.75 1.81 98.2 0.61 2.3 3.2 2241
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 1ZKC 1.75 24.7 22773 21296 1162 98.62 0.16744 0.16671 0.1765 0.18093 0.1992 RANDOM 25.198
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] 0.65 0.33 0.65 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.863 r_dihedral_angle_4_deg 15.968 r_dihedral_angle_3_deg 12.128 r_dihedral_angle_1_deg 6.167 r_scangle_it 3.595 r_scbond_it 2.368 r_angle_refined_deg 1.538 r_mcangle_it 1.289 r_mcbond_it 0.855 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.863 r_dihedral_angle_4_deg 15.968 r_dihedral_angle_3_deg 12.128 r_dihedral_angle_1_deg 6.167 r_scangle_it 3.595 r_scbond_it 2.368 r_angle_refined_deg 1.538 r_mcangle_it 1.289 r_mcbond_it 0.855 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.212 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1333 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing ARP/wARP model building