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_dihedral_angle_d 15.576
f_plane_restr 0.004
f_chiral_restr 0.067
f_angle_d 0.949
f_bond_d 0.005
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALA version: 3.2.25 data reduction