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oligopeptide-binding protein OppA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 100 mM sodium HEPES, 1.0 M tri-sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.494 α = 90 b = 190.494 β = 90 c = 133.269 γ = 90
Symmetry Space Group I 4 2 2
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 BRUKER SMART 6500 2012-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.9789 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.9 39.2 13.4 37769
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 50 35879 1889 99.8 0.21055 0.20901 0.2127 0.23928 0.2366 RANDOM 60.952
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] -2.88 -2.88 5.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 20.326 r_dihedral_angle_3_deg 16.49 r_long_range_B_refined 6.446 r_dihedral_angle_1_deg 6.42 r_long_range_B_other 6.406 r_mcangle_it 4.075 r_mcangle_other 4.074 r_scangle_other 3.74 r_mcbond_it 2.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 20.326 r_dihedral_angle_3_deg 16.49 r_long_range_B_refined 6.446 r_dihedral_angle_1_deg 6.42 r_long_range_B_other 6.406 r_mcangle_it 4.075 r_mcangle_other 4.074 r_scangle_other 3.74 r_mcbond_it 2.465 r_mcbond_other 2.465 r_scbond_it 2.157 r_scbond_other 2.157 r_angle_refined_deg 1.139 r_angle_other_deg 0.761 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5162 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing