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Crystal structure of Lactococcal OppA co-crystallized with Neuropeptide S in an open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M NaCl, 0.1M Na-Hepes, 20% PEG 6000, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.622 α = 90 b = 123.126 β = 102.31 c = 59.281 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 100 CCD ADSC Q210 2007-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.7 42.18 90.1 0.059 11.01 54564 -3 25.03
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 1.7 1.81 76.5 0.405 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DRF 1.8 32.77 47251 2518 97.1 0.19693 0.19425 0.2481 0.2753 RANDOM 15.233
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] -0.07 0.13 -0.84 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 24.748 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 6.488 r_scangle_it 2.585 r_scbond_it 1.665 r_angle_refined_deg 1.238 r_mcangle_it 1.031 r_angle_other_deg 0.852 r_mcbond_it 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 24.748 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 6.488 r_scangle_it 2.585 r_scbond_it 1.665 r_angle_refined_deg 1.238 r_mcangle_it 1.031 r_angle_other_deg 0.852 r_mcbond_it 0.58 r_mcbond_other 0.144 r_chiral_restr 0.073 r_bond_refined_d 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4387 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction