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Initial Events in the Photocycle of Photoactive Yellow Protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K
Crystal Properties Matthews coefficient Solvent content 1.72 20
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.922 α = 90 b = 65.922 β = 90 c = 40.584 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 85 CCD ADSC CCD BENT MIRROR 2002-03-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393,0.9796 ESRF ID14-4
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 1.2 30 98.3 0.035 14.6 4.7 146753 -3
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 1.2 1.23 94.4 0.199 4.5 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.2 40 29323 1559 98.2 0.137 0.136 0.157 RANDOM 10.61
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.586 r_scangle_it 4.084 r_angle_other_deg 4.017 r_scbond_it 2.816 r_mcangle_it 2.21 r_angle_refined_deg 1.979 r_mcbond_it 1.46 r_nbd_refined 0.432 r_nbd_other 0.292 r_symmetry_vdw_other 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.586 r_scangle_it 4.084 r_angle_other_deg 4.017 r_scbond_it 2.816 r_mcangle_it 2.21 r_angle_refined_deg 1.979 r_mcbond_it 1.46 r_nbd_refined 0.432 r_nbd_other 0.292 r_symmetry_vdw_other 0.285 r_symmetry_hbond_refined 0.266 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.219 r_nbtor_other 0.198 r_chiral_restr 0.113 r_gen_planes_other 0.036 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 970 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHARP phasing