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Structure of a loop C-sheet serpin polymer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PEF PDB ENTRY 2PEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 100MM BIS-TRIS, PH5.8, 14% (W/V) PEG 5000, MONOMETHYL ETHER
Crystal Properties Matthews coefficient Solvent content 1.8 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.895 α = 90 b = 68.669 β = 93.45 c = 137.651 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 287 IMAGE PLATE RIGAKU-MSC MIRRORS 2004-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.45 137.3 98.3 0.01 14.4 3.4 28981 2.2
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 2.45 91.8 0.05 2.2 2.9
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 PDB ENTRY 2PEF 2.45 137.36 27494 1474 98.1 0.196 0.192 0.194 0.262 0.2584 RANDOM 19.15
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] 0.1 -0.16 0.02 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_3_deg 14.786 r_dihedral_angle_4_deg 13.39 r_dihedral_angle_1_deg 5.422 r_scangle_it 3.547 r_scbond_it 2.424 r_mcangle_it 1.518 r_angle_refined_deg 0.989 r_mcbond_it 0.844 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_3_deg 14.786 r_dihedral_angle_4_deg 13.39 r_dihedral_angle_1_deg 5.422 r_scangle_it 3.547 r_scbond_it 2.424 r_mcangle_it 1.518 r_angle_refined_deg 0.989 r_mcbond_it 0.844 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.182 r_nbd_refined 0.177 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 5845 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing