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apo NDM-1 Crystal Structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHG PDB ENTRY 2WHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 .1M lithium sulfate, .63M ammonium sulfate, .05M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.536 α = 70.32 b = 73.904 β = 75.86 c = 77.407 γ = 65.3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2011-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-1
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 2.1 49.21 96 0.083 9 73129 70204 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 89.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2WHG 2.1 43.67 73129 70203 3563 96.03 0.242 0.218 0.2161 0.2183 0.2533 0.2543 RANDOM 28.4509
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] 2.15 -1.18 -1.13 -0.35 0.39 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.441 r_dihedral_angle_4_deg 23.417 r_dihedral_angle_3_deg 17.399 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.924 r_angle_other_deg 4.447 r_scbond_it 2.851 r_mcangle_it 1.842 r_angle_refined_deg 1.737 r_mcbond_it 0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.441 r_dihedral_angle_4_deg 23.417 r_dihedral_angle_3_deg 17.399 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.924 r_angle_other_deg 4.447 r_scbond_it 2.851 r_mcangle_it 1.842 r_angle_refined_deg 1.737 r_mcbond_it 0.938 r_chiral_restr 0.136 r_bond_refined_d 0.026 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8632 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 10
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection DENZO data reduction SCALEPACK data scaling SCALA data scaling