X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details EhUbc5 at 8 mg/mL concentration in buffer containing 50 mM HEPES and 100 mM NaCl was mixed 1:1 and equilibrated against crystallization solution (100 mM Tris, 14% (w/v) polyvinylpyrrolidone K 15, and 0.5 mM cobalt (II) chloride), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.97 α = 90
b = 49.58 β = 90
c = 63.46 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2012-07-16
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM

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
1.6 50 99.3 0.044 -- -- 8.2 20139 19998 1.34 0.0 14.9
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)
1.6 1.61 87.3 0.309 -- 2.8 3.7 --

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 1.6 39.069 -- 1.34 20111 19950 1998 99.2 -- 0.1737 0.1706 0.2022 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 1.6 1.6417 -- 137 1148 0.2057 0.2595 -- 91.0
X Ray Diffraction 1.6417 1.686 -- 138 1243 0.1966 0.2484 -- 99.0
X Ray Diffraction 1.686 1.7357 -- 145 1264 0.1833 0.2134 -- 100.0
X Ray Diffraction 1.7357 1.7917 -- 130 1282 0.1904 0.2243 -- 100.0
X Ray Diffraction 1.7917 1.8557 -- 138 1263 0.1809 0.2508 -- 100.0
X Ray Diffraction 1.8557 1.93 -- 144 1294 0.1792 0.2453 -- 100.0
X Ray Diffraction 1.93 2.0178 -- 147 1273 0.1756 0.2112 -- 100.0
X Ray Diffraction 2.0178 2.1242 -- 140 1284 0.1612 0.2134 -- 100.0
X Ray Diffraction 2.1242 2.2573 -- 144 1286 0.1691 0.1966 -- 100.0
X Ray Diffraction 2.2573 2.4316 -- 142 1288 0.1671 0.204 -- 100.0
X Ray Diffraction 2.4316 2.6762 -- 147 1291 0.1813 0.205 -- 100.0
X Ray Diffraction 2.6762 3.0633 -- 143 1308 0.1748 0.2122 -- 100.0
X Ray Diffraction 3.0633 3.8589 -- 146 1330 0.1651 0.1939 -- 100.0
X Ray Diffraction 3.8589 39.0808 -- 157 1398 0.1584 0.1692 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.099
f_dihedral_angle_d 13.0
f_angle_d 1.504
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1195
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 179

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX AutoMR Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHENIX version: AutoMR model building
HKL-2000 data collection