X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.2
Temperature 298.0
Details 28-30% PEG 6000, 0.1 M Tris, pH 8.2, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.73 α = 90
b = 72.33 β = 90.04
c = 79.49 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-04-14
Diffraction Radiation
Monochromator Protocol
Si-111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM

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
2.24 50 99.2 0.081 -- -- 5.6 -- 37060 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)
2.24 2.33 94.1 0.363 -- -- 4.6 3541

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 2.24 32.919 -- 1.38 37046 37034 1847 98.89 -- 0.188 0.1846 0.2544 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 2.24 2.3053 -- 132 2443 0.2327 0.3135 -- 90.0
X Ray Diffraction 2.3053 2.3731 -- 137 2653 0.2303 0.3501 -- 97.0
X Ray Diffraction 2.3731 2.4497 -- 147 2697 0.2351 0.3286 -- 99.0
X Ray Diffraction 2.4497 2.5372 -- 159 2690 0.2296 0.3006 -- 100.0
X Ray Diffraction 2.5372 2.6387 -- 147 2701 0.2233 0.3433 -- 100.0
X Ray Diffraction 2.6387 2.7588 -- 157 2746 0.214 0.3136 -- 100.0
X Ray Diffraction 2.7588 2.9041 -- 146 2718 0.2034 0.2622 -- 100.0
X Ray Diffraction 2.9041 3.086 -- 123 2718 0.197 0.3099 -- 100.0
X Ray Diffraction 3.086 3.324 -- 144 2735 0.1924 0.2677 -- 100.0
X Ray Diffraction 3.324 3.6582 -- 138 2751 0.1934 0.2572 -- 100.0
X Ray Diffraction 3.6582 4.1866 -- 139 2751 0.156 0.2122 -- 100.0
X Ray Diffraction 4.1866 5.2711 -- 134 2787 0.1334 0.18 -- 100.0
X Ray Diffraction 5.2711 32.9222 -- 144 2797 0.1686 0.2032 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.4419
Anisotropic B[1][1] -2.6269
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.6557
Anisotropic B[2][2] 2.3292
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2977
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.576
f_plane_restr 0.003
f_chiral_restr 0.073
f_angle_d 0.919
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6180
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 375

Software

Computing
Computing Package Purpose
In house software Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction