X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microdialysis
pH 7
Temperature 278.0
Details 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL, MICRODIALYSIS, TEMPERATURE 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.16 α = 92.05
b = 50.91 β = 103.05
c = 92.66 γ = 109.6
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-10-10
Diffraction Radiation
Monochromator Protocol
ROSENBAUM ROCK HIGH RESOLUTION DOUBLE CRYSTAL MONOCHROMATOR, LN2 COOLED, SAGITTAL FOCUSSING 2ND MIRROR, SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9537 APS 19-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 20 86.8 0.049 -- -- 2.6 -- 259214 -- -- 8.8
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.1 1.2 71.0 0.535 -- 2.3 1.86 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.1 20.0 -- -- -- 257968 1292 86.83 -- 0.17678 0.17667 0.19842 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.1 1.128 -- 80 15592 0.358 0.325 -- 71.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.04
Anisotropic B[1][1] 0.58
Anisotropic B[1][2] -0.16
Anisotropic B[1][3] 0.13
Anisotropic B[2][2] 0.86
Anisotropic B[2][3] 0.21
Anisotropic B[3][3] -1.47
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 37.181
r_rigid_bond_restr 4.985
r_scbond_other 2.625
r_bond_refined_d 0.014
r_dihedral_angle_4_deg 13.637
r_scbond_it 2.626
r_sphericity_bonded 9.791
r_angle_refined_deg 1.709
r_gen_planes_other 0.001
r_chiral_restr 0.11
r_gen_planes_refined 0.008
r_angle_other_deg 0.858
r_mcangle_it 1.693
r_long_range_B_other 3.377
r_dihedral_angle_3_deg 11.627
r_bond_other_d 0.001
r_sphericity_free 36.897
r_mcbond_it 1.48
r_dihedral_angle_1_deg 6.032
r_long_range_B_refined 4.45
r_mcangle_other 1.695
r_mcbond_other 1.427
r_scangle_other 2.912
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5570
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 804

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
XDS data reduction
XDS data scaling
REFMAC phasing