X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 100mM MES, 2M NaCl, 100mM NaH2PO4, 100mM KH2PO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.88 α = 90
b = 108.88 β = 90
c = 311.65 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2007-06-15
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3

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
2.2 77.8 100.0 0.068 0.068 -- 30.4 56613 56613 0.0 0.0 41.41
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)
2.2 2.32 100.0 0.604 0.604 1.2 18.3 8094

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
SIRAS 2.2 51.394 -- 0.01 53385 53385 2711 94.6 -- 0.1895 0.188 0.218 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 2.2001 2.2401 -- 135 2265 0.2548 0.3034 -- 83.0
X Ray Diffraction 2.2401 2.2832 -- 122 2350 0.2311 0.2362 -- 85.0
X Ray Diffraction 2.2832 2.3298 -- 133 2378 0.2409 0.2759 -- 86.0
X Ray Diffraction 2.3298 2.3804 -- 111 2456 0.2184 0.2604 -- 88.0
X Ray Diffraction 2.3804 2.4358 -- 162 2511 0.2043 0.2296 -- 92.0
X Ray Diffraction 2.4358 2.4967 -- 151 2524 0.2031 0.2599 -- 92.0
X Ray Diffraction 2.4967 2.5642 -- 142 2576 0.2162 0.2948 -- 94.0
X Ray Diffraction 2.5642 2.6397 -- 126 2631 0.2152 0.2509 -- 93.0
X Ray Diffraction 2.6397 2.7249 -- 149 2639 0.2163 0.2675 -- 95.0
X Ray Diffraction 2.7249 2.8223 -- 121 2696 0.2136 0.2272 -- 97.0
X Ray Diffraction 2.8223 2.9352 -- 136 2738 0.2131 0.2563 -- 97.0
X Ray Diffraction 2.9352 3.0688 -- 139 2748 0.2123 0.2618 -- 98.0
X Ray Diffraction 3.0688 3.2306 -- 148 2779 0.2012 0.2299 -- 99.0
X Ray Diffraction 3.2306 3.433 -- 159 2790 0.192 0.2162 -- 99.0
X Ray Diffraction 3.433 3.6979 -- 137 2828 0.1642 0.2123 -- 99.0
X Ray Diffraction 3.6979 4.0699 -- 142 2839 0.1522 0.1773 -- 99.0
X Ray Diffraction 4.0699 4.6585 -- 150 2887 0.1387 0.1647 -- 100.0
X Ray Diffraction 4.6585 5.8679 -- 175 2912 0.1685 0.1931 -- 100.0
X Ray Diffraction 5.8679 51.4081 -- 173 3127 0.1885 0.2084 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 56.755
Anisotropic B[1][1] 9.621
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.621
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -19.242
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.176
f_angle_d 1.406
f_chiral_restr 0.097
f_bond_d 0.013
f_plane_restr 0.006
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.2793
Luzzati Resolution Cutoff (Low) 51.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4935
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 424

Software

Software
Software Name Purpose
PHENIX refinement
PDB_EXTRACT data extraction version: 3.006
DNA data collection
MOSFLM data reduction
SCALA data scaling
SHARP phasing