X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 48 g/L PEG3350, 15 mL/L PEG400, 24 mL/L isopropanol, 0.05 M HEPES sodium, 0.01 M Tris-HCl, 1.6 mM manganese chloride, 0.64 mM magnesium chloride, 1.5 mM sodium azide, 0.25 mM sodium EDTA, 10 g/L octyl beta-D-glucoside, undecyl-beta-D-maltoside, TTFA

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.95 α = 90
b = 84.3 β = 90
c = 290.19 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 ADSC QUANTUM 315r -- 2004-10-09
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.97430 ALS 8.2.2

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
2.1 50.36 99.6 0.114 -- -- 4.7 -- 100834 -- -3.0 34.29
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)
2.1 2.16 99.6 0.636 -- 2.2 4.56 --

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 2.1 50.36 -- 1.33 -- 100591 2048 99.4 -- 0.235 0.235 0.259 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 2.1 2.1489 -- 139 6489 0.3448 0.3624 -- 99.0
X Ray Diffraction 2.1489 2.2026 -- 135 6472 0.3291 0.4155 -- 99.0
X Ray Diffraction 2.2026 2.2621 -- 149 6472 0.3212 0.3236 -- 99.0
X Ray Diffraction 2.2621 2.3287 -- 144 6474 0.3138 0.4014 -- 99.0
X Ray Diffraction 2.3287 2.4039 -- 129 6485 0.3017 0.3539 -- 99.0
X Ray Diffraction 2.4039 2.4898 -- 123 6502 0.2878 0.3057 -- 99.0
X Ray Diffraction 2.4898 2.5895 -- 132 6487 0.2832 0.3367 -- 99.0
X Ray Diffraction 2.5895 2.7073 -- 128 6526 0.2753 0.3517 -- 99.0
X Ray Diffraction 2.7073 2.85 -- 129 6524 0.2657 0.3441 -- 99.0
X Ray Diffraction 2.85 3.0286 -- 152 6586 0.2633 0.3193 -- 100.0
X Ray Diffraction 3.0286 3.2624 -- 136 6569 0.2484 0.2808 -- 100.0
X Ray Diffraction 3.2624 3.5906 -- 111 6622 0.232 0.271 -- 100.0
X Ray Diffraction 3.5906 4.11 -- 158 6655 0.2099 0.2157 -- 100.0
X Ray Diffraction 4.11 5.1773 -- 136 6717 0.1929 0.183 -- 100.0
X Ray Diffraction 5.1773 50.3705 -- 147 6963 0.1848 0.1957 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.7618
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.51
f_dihedral_angle_d 8.295
f_chiral_restr 0.038
f_bond_d 0.002
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8499
Nucleic Acid Atoms 0
Heterogen Atoms 470
Solvent Atoms 437

Software

Software
Software Name Purpose
PHENIX refinement version: (DEV_3150: ???)
DENZO data reduction
SCALEPACK data scaling
PHASER phasing