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Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LRB PDB ENTRY 3LRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 24-28% PEG400, 2mM Cymal-5, 1mM LDAO, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.071 α = 90 b = 77.204 β = 106.79 c = 104.451 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
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 3 30 93.3 6.8 3.3 25006 24681 1.5 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.11 73.4 2.4 2.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LRB 3 25 23349 23349 1255 92.96 0.24473 0.24328 0.27202 0.2738 RANDOM 47.695
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] -7.01 -1.97 7.67 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_3_deg 20.656 r_dihedral_angle_4_deg 16.245 r_dihedral_angle_1_deg 6.665 r_scangle_it 1.694 r_angle_refined_deg 1.418 r_angle_other_deg 1.063 r_scbond_it 1.024 r_mcangle_it 0.745 r_mcbond_it 0.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_3_deg 20.656 r_dihedral_angle_4_deg 16.245 r_dihedral_angle_1_deg 6.665 r_scangle_it 1.694 r_angle_refined_deg 1.418 r_angle_other_deg 1.063 r_scbond_it 1.024 r_mcangle_it 0.745 r_mcbond_it 0.381 r_chiral_restr 0.094 r_mcbond_other 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 6411 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DNA data collection DENZO data reduction SCALEPACK data scaling