X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.4
Temperature 293.0
Details 30% PEG1000, 100 mM phosphate/citrate, 110 mM Lithium Citrate, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.74 α = 90
b = 77.06 β = 92
c = 92.78 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-06-15
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 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
1.75 50 95.3 -- -- -- -- 76010 72438 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)
1.75 1.774 95.3 -- -- -- -- --

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 1.75 19.863 -- 1.34 -- 68339 3430 95.66 -- 0.1883 0.1864 0.2235 --
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 1.75 1.774 -- 112 2444 0.3451 0.3933 -- 91.0
X Ray Diffraction 1.774 1.7993 -- 121 2515 0.3212 0.3365 -- 92.0
X Ray Diffraction 1.7993 1.8261 -- 141 2512 0.2971 0.3797 -- 93.0
X Ray Diffraction 1.8261 1.8546 -- 118 2557 0.2968 0.2727 -- 93.0
X Ray Diffraction 1.8546 1.885 -- 119 2527 0.286 0.3576 -- 94.0
X Ray Diffraction 1.885 1.9175 -- 144 2555 0.2753 0.3505 -- 94.0
X Ray Diffraction 1.9175 1.9523 -- 132 2513 0.2612 0.3141 -- 94.0
X Ray Diffraction 1.9523 1.9899 -- 123 2588 0.2442 0.2858 -- 95.0
X Ray Diffraction 1.9899 2.0304 -- 133 2568 0.2371 0.3164 -- 95.0
X Ray Diffraction 2.0304 2.0745 -- 132 2569 0.2169 0.246 -- 94.0
X Ray Diffraction 2.0745 2.1227 -- 123 2568 0.2152 0.2643 -- 95.0
X Ray Diffraction 2.1227 2.1758 -- 137 2574 0.2049 0.236 -- 95.0
X Ray Diffraction 2.1758 2.2345 -- 143 2577 0.1939 0.2485 -- 96.0
X Ray Diffraction 2.2345 2.3002 -- 152 2550 0.1939 0.2273 -- 95.0
X Ray Diffraction 2.3002 2.3743 -- 138 2602 0.2004 0.2215 -- 95.0
X Ray Diffraction 2.3743 2.459 -- 149 2575 0.2027 0.2372 -- 96.0
X Ray Diffraction 2.459 2.5573 -- 148 2602 0.2049 0.2642 -- 96.0
X Ray Diffraction 2.5573 2.6734 -- 142 2605 0.2011 0.2453 -- 96.0
X Ray Diffraction 2.6734 2.814 -- 154 2623 0.2032 0.242 -- 97.0
X Ray Diffraction 2.814 2.9897 -- 156 2671 0.1981 0.2291 -- 98.0
X Ray Diffraction 2.9897 3.2197 -- 135 2699 0.1885 0.2374 -- 99.0
X Ray Diffraction 3.2197 3.542 -- 136 2722 0.1642 0.1999 -- 99.0
X Ray Diffraction 3.542 4.0508 -- 138 2707 0.1421 0.197 -- 99.0
X Ray Diffraction 4.0508 5.0893 -- 141 2725 0.1245 0.1509 -- 99.0
X Ray Diffraction 5.0893 19.8642 -- 163 2761 0.1718 0.1778 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0354
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.5145
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0354
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.079
f_dihedral_angle_d 14.64
f_angle_d 1.114
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4453
Nucleic Acid Atoms 0
Heterogen Atoms 88
Solvent Atoms 529

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
ADSC version: Quantum data collection