X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 10% PEG 4000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.99 α = 90
b = 117.99 β = 90
c = 321.54 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
2.76 48.69 92.1285 0.115 -- -- 4.5 128895 118749 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)
2.76 2.81 83.0 -- -- 1.38 3.8 --

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 2.75915 48.6897 -- 0.12 128885 108812 5778 84.4257 -- 0.2037 0.2015 0.2425 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 2.7593 2.804 -- 128 3815 0.3061 0.3542 -- 63.0
X Ray Diffraction 2.804 2.8519 -- 0 4286 0.3024 0.0 -- 71.0
X Ray Diffraction 2.8519 2.9031 -- 562 3862 0.2806 0.3368 -- 64.0
X Ray Diffraction 2.9031 2.9583 -- 0 4544 0.2745 0.0 -- 74.0
X Ray Diffraction 2.9583 3.0179 -- 453 4139 0.2702 0.3331 -- 69.0
X Ray Diffraction 3.0179 3.0826 -- 84 4654 0.2629 0.3117 -- 76.0
X Ray Diffraction 3.0826 3.1532 -- 0 4782 0.2546 0.0 -- 79.0
X Ray Diffraction 3.1532 3.2308 -- 610 4241 0.2494 0.2743 -- 70.0
X Ray Diffraction 3.2308 3.3167 -- 0 4983 0.246 0.0 -- 82.0
X Ray Diffraction 3.3167 3.4124 -- 603 4437 0.2288 0.2646 -- 73.0
X Ray Diffraction 3.4124 3.5203 -- 52 5077 0.2163 0.2787 -- 84.0
X Ray Diffraction 3.5203 3.6433 -- 0 5239 0.2065 0.0 -- 86.0
X Ray Diffraction 3.6433 3.7855 -- 667 4632 0.1988 0.2432 -- 76.0
X Ray Diffraction 3.7855 3.9528 -- 0 5382 0.1901 0.0 -- 88.0
X Ray Diffraction 3.9528 4.1543 -- 696 4826 0.1772 0.2142 -- 79.0
X Ray Diffraction 4.1543 4.4044 -- 3 5623 0.1563 0.2177 -- 93.0
X Ray Diffraction 4.4044 4.7281 -- 0 5768 0.1396 0.0 -- 94.0
X Ray Diffraction 4.7281 5.1746 -- 719 5034 0.1543 0.199 -- 84.0
X Ray Diffraction 5.1746 5.8583 -- 0 5889 0.1789 0.0 -- 96.0
X Ray Diffraction 5.8583 7.1548 -- 734 5091 0.2091 0.2304 -- 84.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.241
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.241
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.4819
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.042
f_dihedral_angle_d 13.279
f_angle_d 0.601
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19454
Nucleic Acid Atoms 0
Heterogen Atoms 295
Solvent Atoms 209

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