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Crystal structure of NDM-1 at pH7.5 with 1 molecule per asymmetric unit (crystallized at succinate pH5.5 and soaked at succinate pH7.5)
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 sodium succinate pH5.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.456 α = 90 b = 59.905 β = 98.14 c = 41.74 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 0.95 50 98.7 0.108 10.6 7.1 125133
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 0.95 0.98 96.1 0.325 3.9
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 0.95 41.32 118845 6266 98.64 0.1293 0.1287 0.136 0.1404 0.1441 RANDOM 9.555
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] -0.34 0.29 -0.67 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.486 r_dihedral_angle_4_deg 20.198 r_sphericity_free 17.146 r_dihedral_angle_3_deg 11.069 r_dihedral_angle_1_deg 6.282 r_sphericity_bonded 5.693 r_rigid_bond_restr 1.739 r_angle_refined_deg 1.234 r_angle_other_deg 0.843 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.486 r_dihedral_angle_4_deg 20.198 r_sphericity_free 17.146 r_dihedral_angle_3_deg 11.069 r_dihedral_angle_1_deg 6.282 r_sphericity_bonded 5.693 r_rigid_bond_restr 1.739 r_angle_refined_deg 1.234 r_angle_other_deg 0.843 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1701 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing