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Crystal structure of NDM-1 at pH7.0 (HEPES) with 2 molecules 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 7 295 0.1M HEPES pH7.0, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 36.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.762 α = 90 b = 73.496 β = 98.13 c = 66.448 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 2011-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97922 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 1.55 50 97.5 0.069 8.2 3.7 55127
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 1.55 1.61 95.7 0.441 3.6
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 1.55 50 52315 2790 96.93 0.1199 0.1179 0.1326 0.1579 0.1648 RANDOM 21.17
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] 0.12 -1.03 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.582 r_sphericity_free 25.109 r_dihedral_angle_4_deg 15.773 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.229 r_sphericity_bonded 5.752 r_angle_refined_deg 1.429 r_angle_other_deg 0.927 r_rigid_bond_restr 0.79 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.582 r_sphericity_free 25.109 r_dihedral_angle_4_deg 15.773 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.229 r_sphericity_bonded 5.752 r_angle_refined_deg 1.429 r_angle_other_deg 0.927 r_rigid_bond_restr 0.79 r_chiral_restr 0.121 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3572 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 39
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction