X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 1:1 mixture of protein (~12 mg/mL) in 100 mM NaCl, 20 mM TrisHCl, 1 mM DTT, pH 7 and precipatant (Emerald BioSystems) 25% w/v PEG3350, 4% isopropanol, 0.1 M HEPES (pH 7.5) 0.1 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.92 α = 90
b = 287.59 β = 90
c = 91.36 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-04-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9792 NSLS X29A

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
2.56 49.19 100.0 -- -- -- -- 85635 85635 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)
2.556 2.5865 89.0 -- -- -- -- --

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 2.556 49.191 -- 1.34 85635 81546 4089 99.6 -- 0.2348 0.2328 0.2712 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 2.5564 2.5865 -- 125 2362 0.2966 0.3296 -- 89.0
X Ray Diffraction 2.5865 2.618 -- 151 2621 0.2795 0.3419 -- 100.0
X Ray Diffraction 2.618 2.6511 -- 148 2622 0.2733 0.3318 -- 100.0
X Ray Diffraction 2.6511 2.686 -- 166 2662 0.2658 0.2914 -- 100.0
X Ray Diffraction 2.686 2.7228 -- 150 2609 0.2663 0.3071 -- 100.0
X Ray Diffraction 2.7228 2.7617 -- 126 2653 0.2639 0.2982 -- 100.0
X Ray Diffraction 2.7617 2.8029 -- 130 2684 0.2568 0.3314 -- 100.0
X Ray Diffraction 2.8029 2.8467 -- 118 2657 0.2577 0.2761 -- 100.0
X Ray Diffraction 2.8467 2.8934 -- 131 2637 0.269 0.3045 -- 100.0
X Ray Diffraction 2.8934 2.9433 -- 127 2696 0.2709 0.2865 -- 100.0
X Ray Diffraction 2.9433 2.9968 -- 156 2642 0.27 0.319 -- 100.0
X Ray Diffraction 2.9968 3.0544 -- 124 2676 0.2679 0.3155 -- 100.0
X Ray Diffraction 3.0544 3.1168 -- 142 2629 0.275 0.3533 -- 100.0
X Ray Diffraction 3.1168 3.1845 -- 157 2645 0.2685 0.3036 -- 100.0
X Ray Diffraction 3.1845 3.2586 -- 125 2688 0.2694 0.3572 -- 100.0
X Ray Diffraction 3.2586 3.3401 -- 134 2645 0.2653 0.2811 -- 100.0
X Ray Diffraction 3.3401 3.4303 -- 137 2683 0.2465 0.2999 -- 100.0
X Ray Diffraction 3.4303 3.5313 -- 133 2677 0.2409 0.2703 -- 100.0
X Ray Diffraction 3.5313 3.6452 -- 144 2708 0.2357 0.3006 -- 100.0
X Ray Diffraction 3.6452 3.7754 -- 135 2658 0.2339 0.2647 -- 100.0
X Ray Diffraction 3.7754 3.9265 -- 149 2672 0.2276 0.2805 -- 100.0
X Ray Diffraction 3.9265 4.1052 -- 149 2694 0.2175 0.2353 -- 100.0
X Ray Diffraction 4.1052 4.3215 -- 142 2684 0.2051 0.2382 -- 100.0
X Ray Diffraction 4.3215 4.592 -- 153 2694 0.2001 0.2579 -- 100.0
X Ray Diffraction 4.592 4.9463 -- 131 2708 0.198 0.213 -- 100.0
X Ray Diffraction 4.9463 5.4435 -- 136 2746 0.2203 0.2552 -- 100.0
X Ray Diffraction 5.4435 6.2298 -- 144 2729 0.2313 0.2623 -- 100.0
X Ray Diffraction 6.2298 7.8438 -- 165 2770 0.2152 0.226 -- 100.0
X Ray Diffraction 7.8438 49.2002 -- 161 2906 0.1925 0.2368 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.074
f_dihedral_angle_d 17.677
f_angle_d 1.329
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16440
Nucleic Acid Atoms 0
Heterogen Atoms 372
Solvent Atoms 381

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
phaser model building
HKL-2000 data collection