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Photoactive yellow protein 1-25 deletion mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHY PDB ENTRY 2PHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER LIQUOR. CRYSTALS APPEARED AFTER 2-3 DAYS A LARGEST DIMENSION OF 0.4 MM.
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.566 α = 90 b = 82.566 β = 90 c = 63.453 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2000-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.14 17 94.4 0.06 13.5 4 299780
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 1.14 1.18 89.2 0.217 4.3 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R-VALUE PDB ENTRY 2PHY 1.14 17 74065 1096 93 0.1473 0.1473 0.1559 0.1774 0.1751 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 7 1459 1919
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.067 s_zero_chiral_vol 0.063 s_approx_iso_adps 0.06 s_anti_bump_dis_restr 0.052 s_similar_adp_cmpnt 0.032 s_from_restr_planes 0.0304 s_angle_d 0.027 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1576 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 22
Software Software Software Name Purpose SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling SHELX phasing