X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details 100 mM Na citrate, 15 % (w/v) PEG 6000, and 4% MPD, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.87 α = 90
b = 87.26 β = 90
c = 110.95 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 monochromator 2010-04-18
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID

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 68.59 95.4 0.222 -- -- 5.6 25867 24684 0.0 0.0 18.7
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)
2.05 2.09 83.8 0.599 -- -- 2.7 1044

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 38.347 0.0 0.0 24766 -- 1239 95.41 0.1536 0.1536 0.151 0.203 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 2.0444 2.1263 2231 123 2231 0.1792 0.232 -- 84.0
X Ray Diffraction 2.1263 2.2231 2383 129 2383 0.176 0.2389 -- 89.0
X Ray Diffraction 2.2231 2.3402 2515 128 2515 0.1771 0.2733 -- 94.0
X Ray Diffraction 2.3402 2.4868 2620 134 2620 0.1763 0.2352 -- 97.0
X Ray Diffraction 2.4868 2.6788 2672 141 2672 0.1626 0.2487 -- 99.0
X Ray Diffraction 2.6788 2.9483 2687 143 2687 0.1588 0.2033 -- 99.0
X Ray Diffraction 2.9483 3.3747 2707 143 2707 0.1467 0.2091 -- 99.0
X Ray Diffraction 3.3747 4.2509 2743 144 2743 0.1216 0.1699 -- 99.0
X Ray Diffraction 4.2509 38.3536 2877 154 2877 0.1405 0.1594 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.3523
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.08
f_dihedral_angle_d 13.338
f_bond_d 0.011
f_plane_restr 0.006
f_angle_d 1.327
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2426
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 247

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.8_1062
PDB_EXTRACT data extraction version: 3.11
HKL-3000 data collection
HKL-3000 data reduction
HKL-3000 data scaling