X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_plane_restr 0.003
f_bond_d 0.005
f_chiral_restr 0.073
f_angle_d 0.919
f_dihedral_angle_d 12.576
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.11
PHASER phasing