X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 2.4 M sodium malonate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 166.15 α = 90
b = 203.26 β = 90
c = 143.32 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS VII mirrors 2003-10-09
Diffraction Radiation
Monochromator Protocol
confocal optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-D 1.5418 -- --

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
2.1 50 99.8 -- 0.121 -- 3.5 -- 140272 -- -- 20.6
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)
2.1 2.18 99.6 -- 0.508 2.3 3.2 13842

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 2.1 41.492 -- 0.02 -- 135446 6759 96.34 -- 0.1737 0.1716 0.2136 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 2.1 2.1243 -- 201 4007 0.2522 0.2955 -- 91.0
X Ray Diffraction 2.1243 2.1493 -- 210 4129 0.2443 0.2989 -- 93.0
X Ray Diffraction 2.1493 2.1756 -- 214 4091 0.2418 0.267 -- 93.0
X Ray Diffraction 2.1756 2.2031 -- 223 4143 0.2362 0.2723 -- 94.0
X Ray Diffraction 2.2031 2.2321 -- 232 4159 0.2402 0.2759 -- 94.0
X Ray Diffraction 2.2321 2.2627 -- 237 4163 0.2283 0.2788 -- 94.0
X Ray Diffraction 2.2627 2.295 -- 187 4156 0.2208 0.2761 -- 94.0
X Ray Diffraction 2.295 2.3292 -- 221 4183 0.2116 0.2476 -- 94.0
X Ray Diffraction 2.3292 2.3656 -- 213 4220 0.2202 0.2828 -- 95.0
X Ray Diffraction 2.3656 2.4044 -- 221 4189 0.2144 0.275 -- 95.0
X Ray Diffraction 2.4044 2.4459 -- 248 4203 0.2139 0.2534 -- 95.0
X Ray Diffraction 2.4459 2.4903 -- 229 4242 0.209 0.2766 -- 96.0
X Ray Diffraction 2.4903 2.5382 -- 214 4276 0.2076 0.2625 -- 96.0
X Ray Diffraction 2.5382 2.59 -- 257 4208 0.203 0.2475 -- 96.0
X Ray Diffraction 2.59 2.6463 -- 243 4238 0.2002 0.2567 -- 96.0
X Ray Diffraction 2.6463 2.7079 -- 217 4238 0.1965 0.2568 -- 96.0
X Ray Diffraction 2.7079 2.7756 -- 217 4338 0.1816 0.2439 -- 97.0
X Ray Diffraction 2.7756 2.8506 -- 219 4323 0.1773 0.2168 -- 97.0
X Ray Diffraction 2.8506 2.9345 -- 223 4350 0.1812 0.2071 -- 98.0
X Ray Diffraction 2.9345 3.0292 -- 243 4332 0.1711 0.2141 -- 98.0
X Ray Diffraction 3.0292 3.1374 -- 241 4368 0.1604 0.2195 -- 98.0
X Ray Diffraction 3.1374 3.263 -- 220 4374 0.1507 0.1915 -- 99.0
X Ray Diffraction 3.263 3.4114 -- 237 4414 0.1401 0.1809 -- 99.0
X Ray Diffraction 3.4114 3.5912 -- 242 4398 0.1382 0.1823 -- 99.0
X Ray Diffraction 3.5912 3.816 -- 231 4455 0.13 0.1611 -- 99.0
X Ray Diffraction 3.816 4.1104 -- 217 4430 0.1222 0.1629 -- 99.0
X Ray Diffraction 4.1104 4.5236 -- 231 4469 0.1147 0.1438 -- 99.0
X Ray Diffraction 4.5236 5.1771 -- 228 4458 0.12 0.1398 -- 99.0
X Ray Diffraction 5.1771 6.5185 -- 217 4508 0.1446 0.175 -- 99.0
X Ray Diffraction 6.5185 41.5006 -- 226 4625 0.1668 0.1977 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 25.7
Anisotropic B[1][1] -1.4361
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.0683
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.2778
RMS Deviations
Key Refinement Restraint Deviation
f_angle_deg 1.159
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11140
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 1621

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.4_4) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.4_4) refinement
MOLREP model building
CrystalClear data collection