☰ Navigation Tabs
Crystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule per asymmetric unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1M sodium succinate pH6.5, 40% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.445 α = 90 b = 59.805 β = 97.73 c = 42.132 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 315r 2012-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97930 SSRF BL17U1
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 0.98 50 93.5 0.095 12.7 7.8 109068
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 0.98 1.02 74.1 0.29 6.1
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 3Q6X 0.98 41.75 103572 5462 93.55 0.1204 0.1196 0.1276 0.1352 0.1444 RANDOM 9.824
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] -0.06 -0.09 -0.24 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.721 r_sphericity_free 22.25 r_dihedral_angle_4_deg 19.767 r_dihedral_angle_3_deg 11.818 r_sphericity_bonded 7.466 r_dihedral_angle_1_deg 6.219 r_rigid_bond_restr 2.445 r_angle_refined_deg 1.188 r_angle_other_deg 0.86 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.721 r_sphericity_free 22.25 r_dihedral_angle_4_deg 19.767 r_dihedral_angle_3_deg 11.818 r_sphericity_bonded 7.466 r_dihedral_angle_1_deg 6.219 r_rigid_bond_restr 2.445 r_angle_refined_deg 1.188 r_angle_other_deg 0.86 r_chiral_restr 0.074 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1697 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing