X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.9
Temperature 277.0
Details 20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.78 α = 90
b = 97.78 β = 90
c = 202.74 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-12-09
Diffraction Radiation
Monochromator Protocol
Si(220) side bounce SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E

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
2.57 84.68 96.9 0.027 -- -- 6.4 18985 18978 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)
2.57 2.64 92.3 0.409 -- 5.3 5.7 --

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 2.571 48.888 -- 0.0 -- 18581 1861 97.89 -- 0.212 0.2062 0.2629 --
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 2.571 2.6405 -- 131 1186 0.2755 0.3325 -- 93.0
X Ray Diffraction 2.6405 2.7182 -- 134 1202 0.251 0.3287 -- 94.0
X Ray Diffraction 2.7182 2.8059 -- 134 1217 0.2433 0.2866 -- 95.0
X Ray Diffraction 2.8059 2.9062 -- 136 1227 0.2336 0.3247 -- 96.0
X Ray Diffraction 2.9062 3.0225 -- 142 1250 0.2331 0.2899 -- 97.0
X Ray Diffraction 3.0225 3.16 -- 145 1281 0.2168 0.3105 -- 99.0
X Ray Diffraction 3.16 3.3266 -- 141 1275 0.2151 0.2942 -- 100.0
X Ray Diffraction 3.3266 3.535 -- 145 1308 0.2051 0.2975 -- 100.0
X Ray Diffraction 3.535 3.8078 -- 145 1300 0.2017 0.2717 -- 100.0
X Ray Diffraction 3.8078 4.1908 -- 145 1312 0.1846 0.2168 -- 100.0
X Ray Diffraction 4.1908 4.7968 -- 148 1338 0.1621 0.2185 -- 100.0
X Ray Diffraction 4.7968 6.0417 -- 151 1355 0.2028 0.2515 -- 100.0
X Ray Diffraction 6.0417 48.8968 -- 164 1469 0.2168 0.2422 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Anisotropic B[1][1] 7.1822
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.1822
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.6368
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_bond_d 0.017
f_chiral_restr 0.077
f_dihedral_angle_d 18.691
f_angle_d 1.37
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.3308
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2974
Nucleic Acid Atoms 325
Heterogen Atoms 46
Solvent Atoms 146

Software

Software
Software Name Purpose
HKL-2000 data collection
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.7.3_928)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing