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Crystal structure of NDM-1 at pH7.5 (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 7.5 295 0.1M HEPES pH7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 35.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.691 α = 90 b = 73.475 β = 98.23 c = 66.461 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 2011-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97941 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 1.2 50 99.4 0.06 10.9 7 119756
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 1.2 1.22 98.9 0.444 6.7
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 1.2 50 113625 6005 99.15 0.1153 0.1144 0.114 0.1329 0.1324 RANDOM 14.018
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] -0.09 -0.06 -0.2 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.618 r_sphericity_free 22.197 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 6.382 r_sphericity_bonded 5.373 r_angle_refined_deg 1.385 r_angle_other_deg 0.937 r_rigid_bond_restr 0.838 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.618 r_sphericity_free 22.197 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 6.382 r_sphericity_bonded 5.373 r_angle_refined_deg 1.385 r_angle_other_deg 0.937 r_rigid_bond_restr 0.838 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 656 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction