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Crystal structure of PYP E46Q 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 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.71 27.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.352 α = 90 b = 40.352 β = 90 c = 118.001 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 MARRESEARCH 2003-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.650 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.2 35 94.5 0.037 18.1 8.3 33512 31902 14.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.2 1.24 82.4 0.368 3.4 5.6 3170
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-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PHY 1.2 34.92 31742 31742 1699 0.16658 0.16658 0.16523 0.19113 0.2227 RANDOM 14.293
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] 0.49 0.25 0.49 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.941 r_scangle_it 3.243 r_sphericity_free 2.973 r_sphericity_bonded 2.835 r_scbond_it 2.141 r_mcangle_it 1.853 r_angle_refined_deg 1.44 r_mcbond_it 1.187 r_rigid_bond_restr 1.15 r_angle_other_deg 0.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.941 r_scangle_it 3.243 r_sphericity_free 2.973 r_sphericity_bonded 2.835 r_scbond_it 2.141 r_mcangle_it 1.853 r_angle_refined_deg 1.44 r_mcbond_it 1.187 r_rigid_bond_restr 1.15 r_angle_other_deg 0.806 r_nbd_other 0.291 r_nbd_refined 0.287 r_symmetry_hbond_refined 0.25 r_xyhbond_nbd_refined 0.243 r_symmetry_vdw_other 0.212 r_symmetry_vdw_refined 0.156 r_nbtor_other 0.1 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 966 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing