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Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 165 mM ammonium acetate, and 24% (w/v) PEG 4000, pH 5.6
Crystal Properties Matthews coefficient Solvent content 3.32 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.135 α = 90 b = 170.941 β = 90.02 c = 156.003 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 QUANTUM 4 2006-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.500 NSLS X12B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.58 39.52 99.7 0.07636 0.0907 0.0907 3.4 228105
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 2.58 2.672 97.54 0.3614 3.56 3.3
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 2NPG 2.58 39.52 214711 11219 98.74 0.17307 0.17126 0.1757 0.20822 0.2112 RANDOM 38.18
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] -13.72 8.63 31.08 -17.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 19.283 r_dihedral_angle_3_deg 15.188 r_long_range_B_refined 9.145 r_long_range_B_other 9.145 r_scangle_other 6.877 r_mcangle_it 5.887 r_mcangle_other 5.887 r_dihedral_angle_1_deg 5.839 r_scbond_it 4.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 19.283 r_dihedral_angle_3_deg 15.188 r_long_range_B_refined 9.145 r_long_range_B_other 9.145 r_scangle_other 6.877 r_mcangle_it 5.887 r_mcangle_other 5.887 r_dihedral_angle_1_deg 5.839 r_scbond_it 4.583 r_scbond_other 4.583 r_mcbond_it 4.037 r_mcbond_other 4.037 r_angle_refined_deg 1.747 r_angle_other_deg 1.649 r_chiral_restr 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.009 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 38920 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 720
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing