☰ Navigation Tabs
Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hydrolyzed ampicillin
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 5.5 295 0.1M Bis-Tris pH5.5, 0.2M Li2SO4, 25% PEG 3350, 20 mg/ml ampicillin
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.204 α = 90 b = 79.071 β = 90 c = 133.974 γ = 90
Symmetry Space Group P 21 21 21
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 2011-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.82653 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 1 50 99.2 0.069 9.2 3.8 223485
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 1 1.04 99.8 0.598 3.1
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 1 50 187165 9847 87.41 0.1285 0.1276 0.1265 0.1451 0.1428 RANDOM 22.698
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] -0.67 0.47 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.648 r_sphericity_free 23.218 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 11.902 r_sphericity_bonded 7.854 r_dihedral_angle_1_deg 5.998 r_angle_refined_deg 1.465 r_rigid_bond_restr 1.293 r_angle_other_deg 0.944 r_chiral_restr 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.648 r_sphericity_free 23.218 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 11.902 r_sphericity_bonded 7.854 r_dihedral_angle_1_deg 5.998 r_angle_refined_deg 1.465 r_rigid_bond_restr 1.293 r_angle_other_deg 0.944 r_chiral_restr 0.25 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3596 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction PHASER phasing