X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 12% PEG 3350, 0.12M NH4-Acetate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.74 α = 90
b = 70.41 β = 89.92
c = 84.58 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD TOROIDAL MIRROR 2005-07-05
Diffraction Radiation
Monochromator Protocol
SILICON (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97590 ESRF ID23-1

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
1.92 27 97.8 0.081 -- -- 3.7 -- 60012 0.0 0.0 --
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)
1.92 1.95 81.2 0.356 -- -- 2.6 2501

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 1.92 26.692 0.0 1.35 59996 59996 2544 97.44 -- 0.1807 0.1792 0.2329 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 1.92 1.9602 -- 90 2580 0.2881 0.3133 -- 75.0
X Ray Diffraction 1.9602 2.0002 -- 155 3146 0.2649 0.3097 -- 92.0
X Ray Diffraction 2.0002 2.0437 -- 134 3143 0.2503 0.2782 -- 94.0
X Ray Diffraction 2.0437 2.0911 -- 136 3222 0.229 0.3169 -- 94.0
X Ray Diffraction 2.0911 2.1434 -- 146 3203 0.2399 0.304 -- 94.0
X Ray Diffraction 2.1434 2.2012 -- 134 3232 0.2301 0.2351 -- 95.0
X Ray Diffraction 2.2012 2.2659 -- 132 3179 0.2186 0.2785 -- 95.0
X Ray Diffraction 2.2659 2.3389 -- 149 3221 0.2213 0.3016 -- 94.0
X Ray Diffraction 2.3389 2.4223 -- 138 3196 0.2206 0.2931 -- 94.0
X Ray Diffraction 2.4223 2.5191 -- 136 3243 0.2219 0.2641 -- 95.0
X Ray Diffraction 2.5191 2.6335 -- 143 3212 0.2139 0.2287 -- 95.0
X Ray Diffraction 2.6335 2.7719 -- 132 3255 0.2049 0.2546 -- 95.0
X Ray Diffraction 2.7719 2.945 -- 142 3245 0.1939 0.2304 -- 95.0
X Ray Diffraction 2.945 3.1714 -- 142 3261 0.1708 0.2444 -- 95.0
X Ray Diffraction 3.1714 3.4887 -- 140 3255 0.1524 0.2017 -- 95.0
X Ray Diffraction 3.4887 3.9894 -- 138 3245 0.1292 0.2165 -- 95.0
X Ray Diffraction 3.9894 5.0107 -- 150 3305 0.1132 0.2 -- 95.0
X Ray Diffraction 5.0107 18.8974 -- 148 3316 0.1439 0.1612 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.0886
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.575
f_plane_restr 0.005
f_chiral_restr 0.07
f_angle_d 1.069
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5922
Nucleic Acid Atoms 0
Heterogen Atoms 88
Solvent Atoms 613

Software

Computing
Computing Package Purpose
DNA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
MOLREP molecular replacement
HKL data reduction