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X-RAY DIFFRACTION
Materials and Methods page
2PNM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 291.0
    Details 0.1M Tris-HCl pH 8.5, 22% PEG 2000 MME, 0.45M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 76.95 α = 90
    b = 76.95 β = 90
    c = 136.35 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Details mirrors
    Collection Date 2006-04-23
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X8C
    Wavelength List 0.9792
    Site NSLS
    Beamline X8C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.3
    Resolution(Low) 47.7
    Number Reflections(All) 11248
    Number Reflections(Observed) 11248
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.076
    Redundancy 11.5
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.42
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.186
    Mean I Over Sigma(Observed) 9.8
    Redundancy 11.9
    Number Unique Reflections(All) 1584
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.3
    Resolution(Low) 25.52
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 11248
    Number of Reflections(Observed) 11186
    Number of Reflections(R-Free) 538
    Percent Reflections(Observed) 99.84
    R-Factor(All) 0.2
    R-Factor(Observed) 0.184
    R-Work 0.182
    R-Free 0.235
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 23.945
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.01
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(Observed) 794
    Number of Reflections(R-Free) 44
    Number of Reflections(R-Work) 750
    R-Factor(R-Work) 0.17
    R-Factor(R-Free) 0.234
    Percent Reflections(Observed) 99.75
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.91
    r_scbond_it 2.001
    r_mcangle_it 1.434
    r_mcbond_it 0.924
    r_symmetry_hbond_refined 0.22
    r_bond_refined_d 0.015
    r_angle_refined_deg 1.476
    r_dihedral_angle_1_deg 5.954
    r_dihedral_angle_2_deg 39.848
    r_dihedral_angle_3_deg 14.255
    r_dihedral_angle_4_deg 5.175
    r_chiral_restr 0.1
    r_gen_planes_refined 0.005
    r_nbd_refined 0.214
    r_nbtor_refined 0.307
    r_xyhbond_nbd_refined 0.179
    r_symmetry_vdw_refined 0.22
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1337
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 159
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SHARP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 2.000
    refinement REFMAC5 version: 5.2.0019