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Crystallographic Structure of SurA fragment lacking the second peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M5Y PDB ENTRY 1M5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.4~1.8M sodium chloride, 0.1M potassium dihydrogen phosphate, 0.1 M sodium dihydrogen phosphate, 0.1M MES buffer, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.33 α = 90 b = 148.33 β = 90 c = 188.68 γ = 120
Symmetry Space Group P 32 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 325 mm CCD 2006-06-21 M MAD 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1 2 SYNCHROTRON ALS BEAMLINE 4.2.2 0.9790, 0.9794, 0.9950 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.39 50 99.1 0.074 17.5 4.2 33486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.39 3.52 99.8 0.422 3.5 3326
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 MAD THROUGHOUT PDB ENTRY 1M5Y 3.39 50 33271 1690 98.34 0.284 0.284 0.2752 0.299 0.2905 RANDOM 171.417
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] -2.2 -1.1 -2.2 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.546 r_dihedral_angle_3_deg 18.735 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_1_deg 6.702 r_angle_refined_deg 1.28 r_angle_other_deg 0.782 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.21 r_nbtor_refined 0.179 r_nbd_other 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.546 r_dihedral_angle_3_deg 18.735 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_1_deg 6.702 r_angle_refined_deg 1.28 r_angle_other_deg 0.782 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.21 r_nbtor_refined 0.179 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_other 0.149 r_nbtor_other 0.084 r_chiral_restr 0.066 r_xyhbond_nbd_other 0.022 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4529 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data scaling HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling SnB phasing