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X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP, MICROSEEDING 9 295 AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.83 α = 90 b = 66.83 β = 90 c = 40.92 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 295 CCD ADSC QUANTUM 315 2006-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.45 SPring-8 BL41XU
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 1.25 57.83 100 0.058 0.058 21.9 11.1 28967 28967 10.11
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) 1.25 1.32 100 0.356 0.356 7.3 11.3 4176
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 2PHY 1.25 50 28950 28950 1448 100 0.1122 0.1058 0.1488 0.1438 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 10 1107
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.116 s_approx_iso_adps 0.104 s_zero_chiral_vol 0.08 s_similar_adp_cmpnt 0.042 s_anti_bump_dis_restr 0.031 s_angle_d 0.03 s_from_restr_planes 0.0289 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1019 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 11
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement ADSC data collection XDS data reduction SCALA data scaling AMoRE phasing