X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 3.5
Temperature 291.0
Details EhUbiquitin at 17 mg/mL was mixed 1:1 with and equilibrated against crystallization solution containing 25% (w/v) PEG 3350 and 100 mM citric acid, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.8 α = 90
b = 49.8 β = 90
c = 63.83 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2012-04-08
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B -- APS 23-ID-B

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
1.35 25.65 99.3 0.043 -- -- 19.2 20637 20493 0.0 0.0 19.1
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)
1.35 1.36 100.0 0.557 -- 6.9 17.9 486

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 1.35 25.65 -- 1.38 20654 20454 1028 99.03 -- 0.215 0.212 0.2692 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 1.35 1.4205 2718 143 2718 0.2282 0.3125 -- 98.0
X Ray Diffraction 1.4205 1.5095 -- 147 2752 0.2123 0.3026 -- 100.0
X Ray Diffraction 1.5095 1.6261 -- 145 2757 0.206 0.2783 -- 100.0
X Ray Diffraction 1.6261 1.7897 -- 145 2773 0.2163 0.271 -- 100.0
X Ray Diffraction 1.7897 2.0486 -- 145 2787 0.2044 0.2692 -- 100.0
X Ray Diffraction 2.0486 2.5806 -- 149 2826 0.2243 0.2375 -- 100.0
X Ray Diffraction 2.5806 25.6588 -- 154 2813 0.2078 0.2771 -- 96.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.079
f_dihedral_angle_d 14.6
f_angle_d 1.642
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 546
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 66

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