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Crystal structure of NEAT domain from Staphylococcus aureus in complex with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E7D PDB ENTRY 2E7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 100mM CAPS, 20% polyethylene glycol 8000, 200mM NaCl, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.217 α = 90 b = 75.686 β = 90 c = 39.274 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 210 2007-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
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 1.9 50 98.6 0.069 6.8 11976
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) 1.9 1.97 90.5 0.285 5.9
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 2E7D 1.9 17.62 10756 1168 98.46 0.19747 0.19279 0.1975 0.24175 0.1955 RANDOM 20.495
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.959 r_dihedral_angle_4_deg 26.22 r_dihedral_angle_3_deg 15.924 r_dihedral_angle_1_deg 6.482 r_scangle_it 4.53 r_scbond_it 2.847 r_angle_refined_deg 1.75 r_mcangle_it 1.694 r_mcbond_it 1.198 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.959 r_dihedral_angle_4_deg 26.22 r_dihedral_angle_3_deg 15.924 r_dihedral_angle_1_deg 6.482 r_scangle_it 4.53 r_scbond_it 2.847 r_angle_refined_deg 1.75 r_mcangle_it 1.694 r_mcbond_it 1.198 r_nbtor_refined 0.308 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 908 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing