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Iron reconstituted ferric binding protein from Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4T PDB entry 1Y4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 24% PEG 4000, 0.1M Tris-HCl, 60 mM sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.113 α = 90 b = 54.74 β = 90 c = 92.237 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 100 CCD ADSC QUANTUM 4 Flat mirror (vertical focusing) ; single crystal (311) bent monochromator (horizontal focusing) 2004-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-3 0.974609 SSRL BL11-3
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 1.6 48.8 90.9 0.106 8.6 12.9 38962 13.3
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) 1.6 1.66 73.9 0.196 3
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 1Y4T 1.6 48.8 38897 33603 1771 90.94 0.14677 0.14677 0.14468 0.159 0.18595 0.1961 RANDOM 11.729
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] 0.44 -0.18 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.437 r_scangle_it 4.648 r_scbond_it 2.812 r_mcangle_it 1.582 r_angle_refined_deg 1.581 r_mcbond_it 0.899 r_angle_other_deg 0.876 r_symmetry_vdw_other 0.252 r_nbd_other 0.246 r_nbd_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.437 r_scangle_it 4.648 r_scbond_it 2.812 r_mcangle_it 1.582 r_angle_refined_deg 1.581 r_mcbond_it 0.899 r_angle_other_deg 0.876 r_symmetry_vdw_other 0.252 r_nbd_other 0.246 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.2 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.11 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2505 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing