X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microdialysis
pH 6.7
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+, 10 mm 2,3,4,5,6-pentafluorobenzyl alcohol, 12 to 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278k

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.29 α = 91.72
b = 51.44 β = 103.09
c = 92.49 γ = 110.11
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS 2006-03-09
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL CRYOCOOLED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.9537 APS 23-ID-D

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
1.14 20 93.7 0.065 -- -- 4.75 270489 253394 1.0 1.0 --
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)
1.14 1.18 84.5 0.264 -- 3.2 3.74 --

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 1.14 20.0 -- -- 270489 250826 2572 93.65 -- 0.12406 0.12387 0.14373 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 1.14 1.17 -- 177 16277 0.266 0.312 -- 82.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.926
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] -0.5
Anisotropic B[1][3] 0.21
Anisotropic B[2][2] 0.26
Anisotropic B[2][3] -0.06
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_mcangle_it 2.191
r_mcbond_it 1.479
r_scangle_it 4.734
r_angle_refined_deg 1.673
r_angle_other_deg 1.003
r_dihedral_angle_2_deg 37.256
r_bond_refined_d 0.013
r_gen_planes_other 0.001
r_scbond_it 3.168
r_mcbond_other 0.521
r_dihedral_angle_1_deg 6.24
r_dihedral_angle_3_deg 11.32
r_gen_planes_refined 0.008
r_sphericity_bonded 9.439
r_rigid_bond_restr 3.422
r_chiral_restr 0.102
r_sphericity_free 31.716
r_dihedral_angle_4_deg 13.883
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5570
Nucleic Acid Atoms 0
Heterogen Atoms 150
Solvent Atoms 1040

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
AMoRE phasing
REFMAC refinement version: 5.5.0102
d*TREK data reduction
d*TREK data scaling