X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Temperature 284.0
Details 2M Sodium Formate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.41 α = 90
b = 70.67 β = 113.39
c = 118.31 γ = 90
Symmetry
Space Group I 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
2 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Mercury 3 Integrated MaxFlux confocal optic --
CCD ADSC QUANTUM 315 -- 2010-06-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1
ROTATING ANODE RIGAKU 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
2.04 56 99.3 0.073 -- -- 3.6 49251 49251 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)
2.04 2.15 99.5 0.415 -- 0.415 3.6 --

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 2.044 33.902 -- 0.0 -- 48842 4918 99.19 -- 0.2041 0.2 0.2401 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 2.044 2.0673 -- 193 1438 0.2591 0.3178 -- 99.0
X Ray Diffraction 2.0673 2.0916 -- 180 1430 0.2494 0.3207 -- 100.0
X Ray Diffraction 2.0916 2.1171 -- 150 1465 0.238 0.265 -- 100.0
X Ray Diffraction 2.1171 2.1439 -- 150 1519 0.2379 0.252 -- 100.0
X Ray Diffraction 2.1439 2.1721 -- 163 1420 0.2253 0.2914 -- 99.0
X Ray Diffraction 2.1721 2.2018 -- 174 1478 0.2295 0.265 -- 100.0
X Ray Diffraction 2.2018 2.2333 -- 171 1440 0.2276 0.2653 -- 100.0
X Ray Diffraction 2.2333 2.2666 -- 162 1495 0.2253 0.297 -- 100.0
X Ray Diffraction 2.2666 2.302 -- 152 1438 0.2256 0.287 -- 99.0
X Ray Diffraction 2.302 2.3398 -- 163 1469 0.2216 0.3099 -- 99.0
X Ray Diffraction 2.3398 2.3801 -- 155 1455 0.2355 0.2912 -- 100.0
X Ray Diffraction 2.3801 2.4234 -- 146 1512 0.2198 0.2702 -- 100.0
X Ray Diffraction 2.4234 2.47 -- 142 1447 0.2348 0.2849 -- 99.0
X Ray Diffraction 2.47 2.5204 -- 163 1488 0.2218 0.2972 -- 100.0
X Ray Diffraction 2.5204 2.5752 -- 169 1423 0.2252 0.2728 -- 100.0
X Ray Diffraction 2.5752 2.635 -- 170 1472 0.2241 0.2684 -- 99.0
X Ray Diffraction 2.635 2.7009 -- 176 1463 0.2085 0.2723 -- 99.0
X Ray Diffraction 2.7009 2.7739 -- 160 1449 0.2088 0.2566 -- 99.0
X Ray Diffraction 2.7739 2.8555 -- 183 1431 0.2057 0.2395 -- 99.0
X Ray Diffraction 2.8555 2.9476 -- 160 1481 0.2085 0.2854 -- 99.0
X Ray Diffraction 2.9476 3.0529 -- 167 1479 0.1984 0.2501 -- 100.0
X Ray Diffraction 3.0529 3.175 -- 164 1434 0.2011 0.2585 -- 99.0
X Ray Diffraction 3.175 3.3194 -- 168 1471 0.1833 0.2161 -- 100.0
X Ray Diffraction 3.3194 3.4943 -- 157 1487 0.1644 0.2181 -- 99.0
X Ray Diffraction 3.4943 3.7129 -- 164 1472 0.1768 0.1849 -- 99.0
X Ray Diffraction 3.7129 3.9992 -- 178 1447 0.1787 0.2197 -- 100.0
X Ray Diffraction 3.9992 4.4009 -- 168 1501 0.1591 0.1907 -- 99.0
X Ray Diffraction 4.4009 5.0359 -- 128 1487 0.1538 0.1886 -- 98.0
X Ray Diffraction 5.0359 6.3379 -- 167 1412 0.206 0.2301 -- 95.0
X Ray Diffraction 6.3379 33.9063 -- 175 1521 0.2483 0.2267 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.347
f_chiral_restr 0.089
f_plane_restr 0.006
f_bond_d 0.008
f_dihedral_angle_d 16.307
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5917
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 287

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.1_1168)
HKL-2000 data reduction
SCALEPACK data scaling