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Structure of Psb29 at 1.55A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 0.1 M trisodium citrate, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.66 α = 90 b = 56.1 β = 105.7 c = 44.55 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2012-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
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 1.38 42.89 98.87 0.113 5.1923 13.56 37960
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 1.38 1.42 98.55 1.77 0.34 12.9
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 5MJO 1.38 42.89 36039 1895 98.74 0.11571 0.11356 0.1138 0.15544 0.1555 RANDOM 17.496
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] 0.4 0.71 -0.18 -0.54
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.786 r_dihedral_angle_2_deg 30.416 r_dihedral_angle_4_deg 17.901 r_sphericity_bonded 14.539 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_1_deg 5.448 r_scbond_other 5.239 r_scbond_it 5.237 r_rigid_bond_restr 5.187 r_scangle_other 4.885
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.786 r_dihedral_angle_2_deg 30.416 r_dihedral_angle_4_deg 17.901 r_sphericity_bonded 14.539 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_1_deg 5.448 r_scbond_other 5.239 r_scbond_it 5.237 r_rigid_bond_restr 5.187 r_scangle_other 4.885 r_long_range_B_refined 4.684 r_long_range_B_other 4.413 r_mcangle_it 2.553 r_mcangle_other 2.552 r_mcbond_other 2.248 r_mcbond_it 2.247 r_angle_refined_deg 2.181 r_angle_other_deg 1.16 r_chiral_restr 0.166 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1504 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing