X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.76 α = 90
b = 117.76 β = 90
c = 318.56 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-08-26
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.0809 NSLS X25

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
2.88 48.56 99.6074 0.132 -- -- 4.6 111822 111383 0.0 0.0 --
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)
2.88 2.98 97.0 -- -- 1.04 3.5 --

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 2.8803 48.5625 -- 0.07 111822 98380 4990 87.9791 -- 0.2405 0.2381 0.2829 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 2.9684 3.0157 -- 573 3149 0.3453 0.3887 -- 66.0
X Ray Diffraction 3.0157 3.0663 -- 23 3702 0.3284 0.341 -- 79.0
X Ray Diffraction 3.0663 3.1204 -- 0 3914 0.3336 0.0 -- 82.0
X Ray Diffraction 3.1204 3.1786 -- 431 3654 0.3013 0.3548 -- 76.0
X Ray Diffraction 3.1786 3.2414 -- 207 3778 0.3045 0.367 -- 81.0
X Ray Diffraction 3.2414 3.3094 -- 0 4056 0.2974 0.0 -- 86.0
X Ray Diffraction 3.3094 3.3835 -- 260 4018 0.286 0.2631 -- 83.0
X Ray Diffraction 3.3835 3.4648 -- 385 3872 0.2754 0.2989 -- 81.0
X Ray Diffraction 3.4648 3.5545 -- 0 4253 0.2723 0.0 -- 91.0
X Ray Diffraction 3.5545 3.6542 -- 60 4201 0.2735 0.2853 -- 89.0
X Ray Diffraction 3.6542 3.7662 -- 634 3672 0.2536 0.3049 -- 78.0
X Ray Diffraction 3.7662 3.8933 -- 0 4396 0.2413 0.0 -- 92.0
X Ray Diffraction 3.8933 4.0395 -- 0 4332 0.2318 0.0 -- 92.0
X Ray Diffraction 4.0395 4.2104 -- 710 3730 0.2234 0.2832 -- 78.0
X Ray Diffraction 4.2104 4.4146 -- 0 4362 0.201 0.0 -- 93.0
X Ray Diffraction 4.4146 4.6651 -- 0 4424 0.1835 0.0 -- 93.0
X Ray Diffraction 4.6651 4.9844 -- 698 3705 0.1885 0.2409 -- 78.0
X Ray Diffraction 4.9844 5.414 -- 0 4424 0.2013 0.0 -- 93.0
X Ray Diffraction 5.414 6.0449 -- 0 4435 0.2269 0.0 -- 94.0
X Ray Diffraction 6.0449 7.1348 -- 711 3725 0.2336 0.268 -- 79.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.4117
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.4117
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8233
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.034
f_dihedral_angle_d 12.201
f_angle_d 0.493
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19175
Nucleic Acid Atoms 0
Heterogen Atoms 192
Solvent Atoms 84

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
Phaser model building
HKL-2000 data collection