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Green fluorescent protein ground states: the influence of a second protonation site near the chromophore
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H6V PDB ENTRY 2H6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 AS, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.886 α = 90 b = 62.933 β = 90 c = 71.035 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 298 CCD MARRESEARCH 2006-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979469 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.82 47.106 97.2 0.066 0.066 8.2 6.3 20710 20710 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.92 97.2 0.387 0.387 1.9 3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2H6V 1.82 47.09 2 20710 20710 1072 96.33 0.16732 0.16632 0.1762 0.18594 RANDOM 19.482
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] -0.69 -0.14 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.932 r_dihedral_angle_3_deg 13.291 r_dihedral_angle_4_deg 11.754 r_dihedral_angle_1_deg 6.402 r_scangle_it 3.525 r_scbond_it 2.645 r_angle_refined_deg 1.578 r_mcangle_it 1.561 r_mcbond_it 1.428 r_angle_other_deg 1.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.932 r_dihedral_angle_3_deg 13.291 r_dihedral_angle_4_deg 11.754 r_dihedral_angle_1_deg 6.402 r_scangle_it 3.525 r_scbond_it 2.645 r_angle_refined_deg 1.578 r_mcangle_it 1.561 r_mcbond_it 1.428 r_angle_other_deg 1.385 r_symmetry_vdw_other 0.311 r_nbd_refined 0.276 r_mcbond_other 0.202 r_nbd_other 0.199 r_symmetry_hbond_refined 0.189 r_symmetry_vdw_refined 0.179 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.116 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1912 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement CCP4 data scaling CCP4 phasing