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Ca2+-dependent type II antifreeze protein (Ca2+-free form)
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 0.1M sodium acetate, 0.25M ammonium sulfate, 8% PEG 3350
The crystal was soaked in crystallizaion solution pH adjusted to 3.0 before data collection.
Crystal Properties Matthews coefficient Solvent content 2.26 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.029 α = 90 b = 66.029 β = 90 c = 50.295 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 1.25 16.4 98.3 0.052 0.052 0.055 8.5 10.1 34554
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 1.25 1.32 98.3 0.234 0.234 0.246 3.2 10.4
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 1.25 16.39 32988 1733 98.12 0.18127 0.17965 0.1908 0.21181 0.2181 RANDOM 15.779
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 30.499 r_dihedral_angle_4_deg 14.456 r_dihedral_angle_3_deg 11.563 r_dihedral_angle_1_deg 7.542 r_long_range_B_refined 4.773 r_long_range_B_other 4.322 r_scangle_other 2.944 r_scbond_it 1.982 r_scbond_other 1.97 r_mcangle_it 1.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.499 r_dihedral_angle_4_deg 14.456 r_dihedral_angle_3_deg 11.563 r_dihedral_angle_1_deg 7.542 r_long_range_B_refined 4.773 r_long_range_B_other 4.322 r_scangle_other 2.944 r_scbond_it 1.982 r_scbond_other 1.97 r_mcangle_it 1.965 r_mcangle_other 1.965 r_angle_refined_deg 1.853 r_mcbond_it 1.415 r_mcbond_other 1.41 r_angle_other_deg 1.13 r_chiral_restr 0.098 r_bond_refined_d 0.016 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 974 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing