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Ca2+-dependent type II antifreeze protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 0.1 M sodium acetate, 0.25 M ammonium sulfate, 8% PEG 3350
The Crystal was soaked in crystallizaion solution containing 2mM CaCl2 and pH adjusted to 7.0 before data collection.
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.952 α = 90 b = 65.952 β = 90 c = 49.794 γ = 120
Symmetry Space Group P 31 2 1
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 210 2005-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.06 21.567 99.7 0.045 0.045 0.048 10.1 10.5 56672
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.06 1.12 100 0.229 0.229 0.241 3.4 10.3
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 2ZIB 1.06 19.04 53860 2873 99.65 0.15502 0.15401 0.1629 0.17418 0.1818 RANDOM 9.774
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.844 r_dihedral_angle_4_deg 13.983 r_dihedral_angle_3_deg 11.003 r_dihedral_angle_1_deg 7.308 r_long_range_B_refined 4.181 r_long_range_B_other 3.571 r_angle_other_deg 2.453 r_scangle_other 2.374 r_angle_refined_deg 1.931 r_scbond_it 1.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.844 r_dihedral_angle_4_deg 13.983 r_dihedral_angle_3_deg 11.003 r_dihedral_angle_1_deg 7.308 r_long_range_B_refined 4.181 r_long_range_B_other 3.571 r_angle_other_deg 2.453 r_scangle_other 2.374 r_angle_refined_deg 1.931 r_scbond_it 1.667 r_scbond_other 1.667 r_mcangle_it 1.382 r_mcangle_other 1.381 r_mcbond_it 0.929 r_mcbond_other 0.908 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 983 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing