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PYP ultra-high resolution of a bacterial photoreceptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 39% PEG 3000, 50 mM Tris pH 9, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.621 α = 90 b = 40.621 β = 90 c = 117.734 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 210 Si(111) channel
Toroidal focusing mirror 2005-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.85 NSLS X6A
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 1.05 40 90.6 0.046 3.5 26677
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) 1.05 1.11 97.7 0.239 0.249 2.4 3.5 7312
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 1NWZ 1.05 30.2 26677 2566 98.68 0.16889 0.16815 0.1756 0.18257 0.1913 RANDOM 11.33
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] 0.17 0.09 0.17 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.479 r_dihedral_angle_3_deg 12.231 r_dihedral_angle_1_deg 5.998 r_sphericity_free 4.847 r_dihedral_angle_4_deg 4.002 r_sphericity_bonded 3.151 r_scangle_it 2.295 r_scbond_it 1.814 r_mcangle_it 1.732 r_angle_refined_deg 1.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.479 r_dihedral_angle_3_deg 12.231 r_dihedral_angle_1_deg 5.998 r_sphericity_free 4.847 r_dihedral_angle_4_deg 4.002 r_sphericity_bonded 3.151 r_scangle_it 2.295 r_scbond_it 1.814 r_mcangle_it 1.732 r_angle_refined_deg 1.397 r_rigid_bond_restr 1.319 r_mcbond_it 1.133 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1297 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing