X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 120mM Tris-HCl, 12% PEG 4000, 800mM NaNO3, 160mM KCl, 50mM L-serine, 50mM Na2S2O3, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.44 α = 102.09
b = 116.37 β = 93.39
c = 124.79 γ = 106.06
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2007-05-31
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 PHOTON FACTORY BL-5A

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
3.25 50 99.3 0.129 0.129 -- 3.9 76007 75475 -- -2.0 --
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)
3.25 3.37 98.6 0.538 0.538 2.05 3.8 --

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 3.252 38.518 -- 1.97 76178 75371 3812 98.94 -- 0.2036 0.2003 0.2661 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 3.2523 3.2934 -- 138 2501 0.3399 0.4392 -- 92.0
X Ray Diffraction 3.2934 3.3367 -- 131 2631 0.316 0.3613 -- 99.0
X Ray Diffraction 3.3367 3.3824 -- 167 2624 0.2973 0.3814 -- 99.0
X Ray Diffraction 3.3824 3.4307 -- 125 2699 0.2634 0.3467 -- 99.0
X Ray Diffraction 3.4307 3.4819 -- 130 2591 0.2656 0.3184 -- 99.0
X Ray Diffraction 3.4819 3.5363 -- 148 2711 0.2558 0.3413 -- 99.0
X Ray Diffraction 3.5363 3.5942 -- 130 2597 0.2498 0.3097 -- 99.0
X Ray Diffraction 3.5942 3.6561 -- 131 2689 0.2322 0.2958 -- 99.0
X Ray Diffraction 3.6561 3.7226 -- 144 2652 0.233 0.3173 -- 99.0
X Ray Diffraction 3.7226 3.7941 -- 140 2635 0.2278 0.3196 -- 99.0
X Ray Diffraction 3.7941 3.8715 -- 156 2668 0.2162 0.2706 -- 99.0
X Ray Diffraction 3.8715 3.9556 -- 144 2628 0.2042 0.2534 -- 99.0
X Ray Diffraction 3.9556 4.0475 -- 128 2654 0.1938 0.27 -- 99.0
X Ray Diffraction 4.0475 4.1486 -- 146 2652 0.1818 0.2366 -- 99.0
X Ray Diffraction 4.1486 4.2606 -- 149 2637 0.1785 0.262 -- 99.0
X Ray Diffraction 4.2606 4.3858 -- 141 2691 0.1664 0.2612 -- 99.0
X Ray Diffraction 4.3858 4.5272 -- 135 2653 0.1593 0.2177 -- 99.0
X Ray Diffraction 4.5272 4.6887 -- 134 2695 0.1493 0.2245 -- 99.0
X Ray Diffraction 4.6887 4.8761 -- 132 2670 0.1483 0.2298 -- 99.0
X Ray Diffraction 4.8761 5.0975 -- 152 2640 0.1583 0.253 -- 100.0
X Ray Diffraction 5.0975 5.3656 -- 138 2677 0.1658 0.2309 -- 100.0
X Ray Diffraction 5.3656 5.7008 -- 152 2649 0.1998 0.3042 -- 100.0
X Ray Diffraction 5.7008 6.1393 -- 134 2688 0.2032 0.2975 -- 100.0
X Ray Diffraction 6.1393 6.7542 -- 159 2637 0.2278 0.3148 -- 100.0
X Ray Diffraction 6.7542 7.7247 -- 155 2672 0.1794 0.2604 -- 100.0
X Ray Diffraction 7.7247 9.7065 -- 140 2672 0.1435 0.1816 -- 100.0
X Ray Diffraction 9.7065 38.5209 -- 133 2646 0.2429 0.2453 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 123.292
Anisotropic B[1][1] -40.2921
Anisotropic B[1][2] -0.5608
Anisotropic B[1][3] -7.5529
Anisotropic B[2][2] 41.1022
Anisotropic B[2][3] -2.4413
Anisotropic B[3][3] -0.8101
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.109
f_plane_restr 0.004
f_chiral_restr 0.074
f_angle_d 1.26
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 30803
Nucleic Acid Atoms 0
Heterogen Atoms 85
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction