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R52Q Mutant of 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 6 293 40% PEG2000, 100mM sodium citrate, pH 6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 33.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.02 α = 90 b = 37.02 β = 90 c = 129.62 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 2004-01-01 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 1.42 25.74 99.9 0.07 17 11.1 18879
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 1.42 20 17895 971 99.95 0.1418 0.1406 0.1402 0.16346 0.1341 RANDOM 13.247
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] 0.22 0.11 0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.164 r_dihedral_angle_4_deg 14.554 r_dihedral_angle_3_deg 12.321 r_dihedral_angle_1_deg 5.899 r_sphericity_free 5.017 r_scangle_it 4.012 r_sphericity_bonded 3.235 r_scbond_it 2.811 r_mcangle_it 2.082 r_rigid_bond_restr 1.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.164 r_dihedral_angle_4_deg 14.554 r_dihedral_angle_3_deg 12.321 r_dihedral_angle_1_deg 5.899 r_sphericity_free 5.017 r_scangle_it 4.012 r_sphericity_bonded 3.235 r_scbond_it 2.811 r_mcangle_it 2.082 r_rigid_bond_restr 1.537 r_mcbond_it 1.51 r_angle_refined_deg 1.494 r_nbtor_refined 0.311 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 999 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing