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Wild Type Photoactive Yellow Protein, P65 Form
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 6.5 293 40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.422 α = 90 b = 40.422 β = 90 c = 118.131 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 100 CCD ADSC QUANTUM 4 bending magnet 2004-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 1.000 SPring-8 BL40B2
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 1.34 20.09 99.8 0.053 14.2 11.1 23170
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) 1.34 1.39 99.8 0.303 9.09 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2PHY 1.34 20 23170 1244 99.91 0.15397 0.15209 0.1534 0.18915 0.1548 RANDOM 16.989
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] 0.53 0.27 0.53 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.474 r_dihedral_angle_3_deg 15.769 r_dihedral_angle_4_deg 12.98 r_dihedral_angle_1_deg 6.074 r_sphericity_free 5.36 r_sphericity_bonded 4.264 r_scangle_it 3.615 r_scbond_it 2.857 r_mcangle_it 2.289 r_rigid_bond_restr 2.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.474 r_dihedral_angle_3_deg 15.769 r_dihedral_angle_4_deg 12.98 r_dihedral_angle_1_deg 6.074 r_sphericity_free 5.36 r_sphericity_bonded 4.264 r_scangle_it 3.615 r_scbond_it 2.857 r_mcangle_it 2.289 r_rigid_bond_restr 2.094 r_mcbond_it 1.596 r_angle_refined_deg 1.487 r_nbtor_refined 0.316 r_nbd_refined 0.257 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1025 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing