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1.6 angstrom crystal structure of fluorescent protein Cypet
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QYO PDB ENTRY 1QYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.907 α = 90 b = 63.011 β = 90 c = 71.424 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.6 50 91.1 0.039 16.7 2.3 31080 28302 2 2
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) 1.6 1.66 59.1 0.23 3.2 1.8 1825
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 1QYO 1.6 20.41 25452 2848 91.16 0.19683 0.19324 0.1893 0.22881 0.2257 RANDOM 20.199
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] -0.98 -1.16 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.131 r_dihedral_angle_3_deg 12.043 r_dihedral_angle_4_deg 11.1 r_dihedral_angle_1_deg 6.222 r_scangle_it 1.55 r_mcangle_it 1.502 r_angle_refined_deg 1.309 r_scbond_it 1.013 r_mcbond_it 0.939 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.131 r_dihedral_angle_3_deg 12.043 r_dihedral_angle_4_deg 11.1 r_dihedral_angle_1_deg 6.222 r_scangle_it 1.55 r_mcangle_it 1.502 r_angle_refined_deg 1.309 r_scbond_it 1.013 r_mcbond_it 0.939 r_nbtor_refined 0.317 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1907 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling