X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 291.0
Details EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.63 α = 90
b = 49.87 β = 90
c = 76.82 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 -- 2012-04-08
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.000 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
2.15 40 98.1 0.085 -- -- 3.5 8593 8430 0.0 0.0 32.8
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)
2.15 2.17 96.8 0.279 -- 3.1 3.3 210

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 2.15 34.513 -- 1.34 8591 8379 840 97.53 -- 0.1994 0.1932 0.2561 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 2.15 2.2772 1154 129 1154 0.2658 0.3505 -- 92.0
X Ray Diffraction 2.2772 2.453 -- 135 1213 0.2456 0.3471 -- 97.0
X Ray Diffraction 2.453 2.6997 -- 141 1260 0.2415 0.3361 -- 99.0
X Ray Diffraction 2.6997 3.0902 -- 141 1276 0.2206 0.271 -- 99.0
X Ray Diffraction 3.0902 3.8924 -- 145 1293 0.1768 0.2642 -- 99.0
X Ray Diffraction 3.8924 34.5176 -- 149 1343 0.1598 0.193 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.094
f_dihedral_angle_d 16.107
f_angle_d 1.493
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1165
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 44

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