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X-structure of a variant of NCR from zymomonas mobilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A3U PDB entry 4A3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 292 0.1 M sodium citrate, 1.0 M lithium chloride, 21% PEG 6000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.24 α = 90 b = 121.24 β = 90 c = 58.65 γ = 120
Symmetry Space Group P 31 2 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 PIXEL PSI PILATUS 6M 2013-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
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 1.8 39.7 99.9 0.068 22.49 46089
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 4A3U 1.8 39.7 45627 461 99.88 0.17044 0.17018 0.1818 0.19553 0.199 RANDOM 35.4
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] -1.41 -1.41 -1.41 4.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.613 r_dihedral_angle_4_deg 19.212 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_1_deg 7.223 r_angle_refined_deg 2.051 r_angle_other_deg 0.954 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.613 r_dihedral_angle_4_deg 19.212 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_1_deg 7.223 r_angle_refined_deg 2.051 r_angle_other_deg 0.954 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2419 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 37
Software Software Software Name Purpose MxCuBE data collection ARP/wARP model building REFMAC refinement XDS data reduction XSCALE data scaling