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Crystal structure of the alpha parvalbumin from thornback ray
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2.5 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.72 28.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.199 α = 90 b = 37.725 β = 95.369 c = 38.809 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX300-HS 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 40 95 0.091 0.091 0.108 0.058 0.999 18.7 3.4 9078
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) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.392 0.392 0.478 0.259 0.85 2.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5ZH6 1.75 32.078 9019 415 95.037 0.184 0.1824 0.1933 0.2228 0.2369 17.19
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] -1.577 -0.356 0.642 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.319 r_dihedral_angle_3_deg 11.034 r_dihedral_angle_2_deg 7.82 r_dihedral_angle_1_deg 5.672 r_lrange_it 5.081 r_lrange_other 4.619 r_scangle_other 2.355 r_scangle_it 2.353 r_mcangle_it 1.57 r_mcangle_other 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.319 r_dihedral_angle_3_deg 11.034 r_dihedral_angle_2_deg 7.82 r_dihedral_angle_1_deg 5.672 r_lrange_it 5.081 r_lrange_other 4.619 r_scangle_other 2.355 r_scangle_it 2.353 r_mcangle_it 1.57 r_mcangle_other 1.569 r_scbond_it 1.385 r_scbond_other 1.379 r_angle_refined_deg 1.264 r_mcbond_it 0.949 r_mcbond_other 0.948 r_angle_other_deg 0.491 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.227 r_nbd_other 0.218 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.133 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.066 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 821 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling MOLREP phasing