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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-HCl pH 9, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.779 α = 90 b = 40.779 β = 90 c = 117.576 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 cut monochromator
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 Merge I (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 40 0.045 0.039 3.1 32475
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) 1.2 1.26 71.1 0.24 0.18 2.6 1.4 1115
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 1.2 33.83 30823 1652 94.32 0.19975 0.1987 0.2004 0.21944 0.2096 RANDOM 13.527
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_3_deg 12.425 r_dihedral_angle_1_deg 6.467 r_scangle_it 3.653 r_scbond_it 2.755 r_mcangle_it 1.979 r_angle_refined_deg 1.359 r_mcbond_it 1.321 r_dihedral_angle_4_deg 1.178 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_3_deg 12.425 r_dihedral_angle_1_deg 6.467 r_scangle_it 3.653 r_scbond_it 2.755 r_mcangle_it 1.979 r_angle_refined_deg 1.359 r_mcbond_it 1.321 r_dihedral_angle_4_deg 1.178 r_nbtor_refined 0.314 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.088 r_xyhbond_nbd_refined 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction AMoRE phasing