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Crystal structure of Gallus gallus beta-parvalbumin (avian thymic hormone)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 The reservoir contained 70% saturated ammonium sulfate, 100 micromolar calcium ion, 10 millimolar MES buffer. The volume of the hanging drop was 80 microliters. , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.76 30.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.644 α = 87.42 b = 51.56 β = 85.42 c = 67.633 γ = 87.42
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 315 MD2 micro-diffractometer with 20 micron aperature 2008-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.95 50 98 0.086 16.6 4.3 45451 45451 17
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) 1.95 2.02 96.8 0.42 3.2 4.3 4474
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1RWY 1.9539 35.632 1.98 45451 45426 2288 97.87 0.1663 0.1635 0.1631 0.2206 0.2189 Random 21.218
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] 2.534 0.82 4.831 -2.294 3.079 -0.241
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.7 f_angle_deg 0.715 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6480 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing REFMAC refinement