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Structure of de novo designed apo peptide coil SER L9C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5F PDB ENTRY 3H5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 24% PEG 3350, 0.017M zinc acetate, 0.1M calcium acetate, 0.1M cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.94 α = 90 b = 29.856 β = 119.15 c = 44.361 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 225 mm CCD Diamond Laue 2009-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.36 50 99.4 0.069 20 6.7 19279 19279 10.8
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) 1.36 1.4 100 0.35 5 6 959
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3H5F 1.36 34.03 18278 18278 978 99.23 0.18416 0.18416 0.18241 0.1903 0.2151 0.2157 RANDOM 16.806
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.384 r_dihedral_angle_3_deg 13.574 r_scangle_it 5.634 r_scbond_it 4.144 r_dihedral_angle_1_deg 4.113 r_mcangle_it 2.377 r_angle_refined_deg 2.364 r_mcbond_it 1.35 r_chiral_restr 0.107 r_bond_refined_d 0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.384 r_dihedral_angle_3_deg 13.574 r_scangle_it 5.634 r_scbond_it 4.144 r_dihedral_angle_1_deg 4.113 r_mcangle_it 2.377 r_angle_refined_deg 2.364 r_mcbond_it 1.35 r_chiral_restr 0.107 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 702 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 18
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling