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S100Z from zebrafish in complex with calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CGA PDB ENTRY 3CGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.1M SODIUM ACETATE; 10% PEG 1.5K; 0.2M CACL2, 20% ISOPROPANOL., pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.155 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.611 α = 90 b = 132.25 β = 90 c = 58.209 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 120 CCD ADSC QUANTUM 210 2004-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.03 66.1 98.8 0.1 24.3 10.3 38644 2
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 2.03 85.1 0.34 5.8
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 PDB ENTRY 3CGA 2.03 66.13 36265 1909 98.81 0.1737 0.17092 0.1791 0.22677 0.2062 RANDOM 21.577
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] -0.26 1.5 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_3_deg 15.782 r_dihedral_angle_4_deg 8.418 r_dihedral_angle_1_deg 5.553 r_angle_refined_deg 1.583 r_angle_other_deg 0.98 r_chiral_restr 0.099 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_3_deg 15.782 r_dihedral_angle_4_deg 8.418 r_dihedral_angle_1_deg 5.553 r_angle_refined_deg 1.583 r_angle_other_deg 0.98 r_chiral_restr 0.099 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4548 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing