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crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino Acid PYZ151
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.9 289 60~100mg/ml protein sample in 50 mM Hepes, pH 7.5, reservior solution:17~19% PEG 3000, 100mM Tris pH 8.9,0.2M calcium acetate , VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.827 α = 90 b = 63.052 β = 90 c = 70.369 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 90 CCD ADSC QUANTUM 315 2012-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 1.1 30 99.1 0.088 21.1 6.2 92448 91616 1 1
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 1.1 1.14 99.5 0.342 6.9 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4GES 1.1 30 87901 87031 4576 99.01 0.16667 0.16602 0.1658 0.179 0.1776 RANDOM 11.058
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] 0.02 -0.18 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.773 r_dihedral_angle_3_deg 12.352 r_dihedral_angle_4_deg 8.057 r_dihedral_angle_1_deg 6.218 r_sphericity_free 4.829 r_sphericity_bonded 3.017 r_scangle_it 2.899 r_scbond_it 1.985 r_mcangle_it 1.764 r_angle_refined_deg 1.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.773 r_dihedral_angle_3_deg 12.352 r_dihedral_angle_4_deg 8.057 r_dihedral_angle_1_deg 6.218 r_sphericity_free 4.829 r_sphericity_bonded 3.017 r_scangle_it 2.899 r_scbond_it 1.985 r_mcangle_it 1.764 r_angle_refined_deg 1.465 r_mcbond_it 1.105 r_rigid_bond_restr 1.049 r_chiral_restr 0.106 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1916 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing