X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 100 mM HEPES, pH 7.5, 1.4 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.18 α = 90
b = 120.18 β = 90
c = 77.81 γ = 120
Symmetry
Space Group P 31 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-10-29
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9792 ESRF ID23-1

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
2.3 104.08 99.8 -- 0.061 -- 5.8 28423 28423 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)
2.304 2.43 99.0 0.683 0.683 1.1 4.1 4113

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 2.304 32.658 -- 1.35 28423 28396 1438 99.74 -- 0.1709 0.1693 0.2014 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 2.304 2.3866 -- 145 2651 0.3174 0.3479 -- 99.0
X Ray Diffraction 2.3866 2.4821 -- 146 2655 0.2989 0.3367 -- 100.0
X Ray Diffraction 2.4821 2.5951 -- 141 2697 0.2563 0.3075 -- 100.0
X Ray Diffraction 2.5951 2.7318 -- 157 2682 0.2159 0.2415 -- 100.0
X Ray Diffraction 2.7318 2.9029 -- 150 2672 0.1867 0.229 -- 100.0
X Ray Diffraction 2.9029 3.1268 -- 138 2707 0.1855 0.1976 -- 100.0
X Ray Diffraction 3.1268 3.4412 -- 157 2678 0.1745 0.2296 -- 100.0
X Ray Diffraction 3.4412 3.9384 -- 137 2711 0.1486 0.1803 -- 100.0
X Ray Diffraction 3.9384 4.9592 -- 128 2745 0.1249 0.1474 -- 100.0
X Ray Diffraction 4.9592 32.661 -- 139 2760 0.1599 0.1779 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.1407
Anisotropic B[1][1] -12.4073
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.4073
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 24.8146
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.093
f_plane_restr 0.004
f_chiral_restr 0.073
f_angle_d 1.059
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2509
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 87

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction