X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 7
Temperature 295.0
Details 2.4M sodium malonate pH 7.0, Microbatch, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 197.76 α = 90
b = 95.21 β = 97.05
c = 99.42 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 203
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
GRAPHITE MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97888, 0.97917, 0.96395, 1.00000 Photon Factory AR-NW12A

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
1.49 50 96.2 -- -- -- -- 297211 285917 3.0 3.0 --
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)
1.49 50.0 96.2 0.316 -- 3.6 3.3 --

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
MAD 1.492 28.555 -- 1.34 297185 285892 14491 96.51 0.15 0.1448 0.1434 0.1695 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 1.492 1.509 -- 403 8463 0.1711 0.2223 -- 90.0
X Ray Diffraction 1.509 1.5268 -- 479 8854 0.164 0.2228 -- 95.0
X Ray Diffraction 1.5268 1.5454 -- 500 8836 0.1447 0.2033 -- 95.0
X Ray Diffraction 1.5454 1.5649 -- 467 8945 0.1389 0.1791 -- 96.0
X Ray Diffraction 1.5649 1.5855 -- 509 8812 0.1288 0.1677 -- 95.0
X Ray Diffraction 1.5855 1.6073 -- 457 8965 0.125 0.1605 -- 96.0
X Ray Diffraction 1.6073 1.6302 -- 503 8931 0.1255 0.1642 -- 96.0
X Ray Diffraction 1.6302 1.6545 -- 498 8981 0.127 0.1722 -- 96.0
X Ray Diffraction 1.6545 1.6804 -- 503 8979 0.1256 0.1655 -- 96.0
X Ray Diffraction 1.6804 1.7079 -- 453 9055 0.1238 0.163 -- 96.0
X Ray Diffraction 1.7079 1.7374 -- 486 9029 0.1249 0.1611 -- 96.0
X Ray Diffraction 1.7374 1.769 -- 495 9068 0.1368 0.1774 -- 97.0
X Ray Diffraction 1.769 1.803 -- 477 9035 0.136 0.1955 -- 97.0
X Ray Diffraction 1.803 1.8398 -- 502 9085 0.1288 0.1597 -- 97.0
X Ray Diffraction 1.8398 1.8798 -- 513 9059 0.1268 0.1608 -- 97.0
X Ray Diffraction 1.8798 1.9235 -- 510 9097 0.1324 0.17 -- 97.0
X Ray Diffraction 1.9235 1.9716 -- 465 9131 0.1343 0.1691 -- 98.0
X Ray Diffraction 1.9716 2.0249 -- 496 9196 0.1362 0.1693 -- 98.0
X Ray Diffraction 2.0249 2.0845 -- 452 9197 0.1299 0.1606 -- 98.0
X Ray Diffraction 2.0845 2.1517 -- 463 9224 0.1273 0.1538 -- 98.0
X Ray Diffraction 2.1517 2.2286 -- 480 9206 0.1307 0.1646 -- 98.0
X Ray Diffraction 2.2286 2.3178 -- 504 9251 0.134 0.1634 -- 99.0
X Ray Diffraction 2.3178 2.4232 -- 506 9282 0.1375 0.1582 -- 99.0
X Ray Diffraction 2.4232 2.5509 -- 517 9308 0.1467 0.1878 -- 99.0
X Ray Diffraction 2.5509 2.7106 -- 471 9306 0.1507 0.1822 -- 99.0
X Ray Diffraction 2.7106 2.9197 -- 452 9398 0.1561 0.1645 -- 99.0
X Ray Diffraction 2.9197 3.2132 -- 471 9364 0.1554 0.1794 -- 99.0
X Ray Diffraction 3.2132 3.6773 -- 504 9223 0.1383 0.1478 -- 98.0
X Ray Diffraction 3.6773 4.6298 -- 473 8746 0.1429 0.1494 -- 93.0
X Ray Diffraction 4.6298 28.56 -- 482 8375 0.1861 0.2019 -- 88.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_angle_d 1.177
f_chiral_restr 0.078
f_dihedral_angle_d 12.701
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10560
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 2111

Software

Software
Software Name Purpose
HKL-2000 data collection
SOLVE phasing
PHENIX refinement version: (phenix.refine: 1.8_1063)
HKL-2000 data reduction
HKL-2000 data scaling