X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 279.0
Details 15.2% PEG4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.72 α = 90
b = 61.83 β = 94.09
c = 92.92 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 99
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2007-02-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 ESRF ID14-3

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
1.9 92.85 94.9 0.057 0.057 -- 3.7 41312 41312 -- -- 23.0
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)
1.9 2.0 78.6 0.253 0.253 2.9 3.5 4978

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 1.9 38.209 -- 1.35 -- 41297 2077 94.64 -- 0.1745 0.1715 0.2304 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 1.9 1.9442 1953 86 1953 0.2164 0.2941 -- 70.0
X Ray Diffraction 1.9442 1.9928 2298 119 2298 0.1999 0.2462 -- 83.0
X Ray Diffraction 1.9928 2.0467 2628 135 2628 0.1898 0.2904 -- 96.0
X Ray Diffraction 2.0467 2.1069 2682 143 2682 0.195 0.2542 -- 97.0
X Ray Diffraction 2.1069 2.1749 2665 133 2665 0.2259 0.32 -- 97.0
X Ray Diffraction 2.1749 2.2526 2650 156 2650 0.2121 0.2829 -- 97.0
X Ray Diffraction 2.2526 2.3428 2650 153 2650 0.1834 0.2645 -- 97.0
X Ray Diffraction 2.3428 2.4494 2719 139 2719 0.1758 0.2612 -- 97.0
X Ray Diffraction 2.4494 2.5785 2673 140 2673 0.1735 0.2456 -- 98.0
X Ray Diffraction 2.5785 2.7401 2694 137 2694 0.1716 0.2437 -- 98.0
X Ray Diffraction 2.7401 2.9515 2704 131 2704 0.1767 0.2345 -- 98.0
X Ray Diffraction 2.9515 3.2484 2743 144 2743 0.162 0.237 -- 98.0
X Ray Diffraction 3.2484 3.7181 2687 159 2687 0.1474 0.2165 -- 98.0
X Ray Diffraction 3.7181 4.6831 2719 147 2719 0.1221 0.1686 -- 98.0
X Ray Diffraction 4.6831 38.2172 2755 155 2755 0.1438 0.1557 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.9196
Anisotropic B[1][1] 1.2065
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.0636
Anisotropic B[2][2] -4.1782
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.9717
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.005
f_plane_restr 0.004
f_chiral_restr 0.067
f_dihedral_angle_d 15.576
f_angle_d 0.949
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4053
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 632

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
PHENIX refinement
PDB_EXTRACT data extraction version: 3.10
MOSFLM data reduction
PHASER phasing