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Crystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.16 M NaH2PO4 x 2H2O, 16% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.87 α = 90 b = 102.87 β = 90 c = 242.53 γ = 120
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 MARMOSAIC 300 mm CCD mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.05 30 99.7 0.078 11 7.6 31372
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 2.05 2.12 98.2 0.562 7.1 3033
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1QY3 2.05 28.7 31367 1581 99.73 0.1989 0.1958 0.2557 0.2752 RANDOM 41.3494
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 39.072 r_dihedral_angle_3_deg 16.885 r_dihedral_angle_4_deg 12.616 r_dihedral_angle_1_deg 7.321 r_scangle_it 4.623 r_scbond_it 3.09 r_mcangle_it 1.983 r_angle_refined_deg 1.872 r_mcbond_it 1.121 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.072 r_dihedral_angle_3_deg 16.885 r_dihedral_angle_4_deg 12.616 r_dihedral_angle_1_deg 7.321 r_scangle_it 4.623 r_scbond_it 3.09 r_mcangle_it 1.983 r_angle_refined_deg 1.872 r_mcbond_it 1.121 r_chiral_restr 0.154 r_bond_refined_d 0.026 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3650 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing