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Structure of NP275, a pentapeptide repeat protein from Nostoc punctiforme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BM5 PDB ENTRY 2BM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 30% PEG3350 100 MM NACACODYLATE PH 6.8 200MM LICL2 PROTEIN 25MG/ML
Crystal Properties Matthews coefficient Solvent content 1.87 33.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.181 α = 90 b = 62.558 β = 90 c = 100.549 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 194 IMAGE PLATE RIGAKU IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.1 26.5 100 0.05 23.6 5.6 11358
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 2.1 2.21 100 0.17 8.1 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BM5 2.1 100.5 10813 544 99.9 0.191 0.188 0.256 0.2981 RANDOM 17.91
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] -1.12 0.98 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.906 r_dihedral_angle_3_deg 15.445 r_dihedral_angle_4_deg 9.2 r_dihedral_angle_1_deg 5.511 r_scangle_it 2.605 r_scbond_it 1.682 r_angle_refined_deg 1.49 r_mcangle_it 0.898 r_mcbond_it 0.521 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.906 r_dihedral_angle_3_deg 15.445 r_dihedral_angle_4_deg 9.2 r_dihedral_angle_1_deg 5.511 r_scangle_it 2.605 r_scbond_it 1.682 r_angle_refined_deg 1.49 r_mcangle_it 0.898 r_mcbond_it 0.521 r_nbtor_refined 0.295 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1644 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing