X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 10% PEG 6000, 5% MPD, 0.1M MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.02 α = 62.31
b = 115.19 β = 77.94
c = 114.99 γ = 81.05
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR MARMOSAIC 225 mm CCD MIRRORS 2010-01-23
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U

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
2.87 50 98.0 0.105 0.105 -- 3.7 -- 64796 -- 1.5 56.27
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)
2.87 3.0 90.7 0.501 0.501 1.9 2.7 --

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 2.872 24.19 -- 0.07 -- 61067 3085 91.6 -- 0.247 0.246 0.27 --
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 2.8716 2.9164 -- 85 1567 0.3254 0.3783 -- 57.0
X Ray Diffraction 2.9164 2.9641 -- 116 2233 0.3179 0.3668 -- 77.0
X Ray Diffraction 2.9641 3.0151 -- 127 2338 0.3152 0.3527 -- 80.0
X Ray Diffraction 3.0151 3.0699 -- 105 2389 0.317 0.3285 -- 84.0
X Ray Diffraction 3.0699 3.1288 -- 123 2541 0.2933 0.3302 -- 86.0
X Ray Diffraction 3.1288 3.1925 -- 147 2503 0.2953 0.3273 -- 88.0
X Ray Diffraction 3.1925 3.2618 -- 137 2574 0.2911 0.3123 -- 90.0
X Ray Diffraction 3.2618 3.3375 -- 132 2652 0.284 0.3183 -- 91.0
X Ray Diffraction 3.3375 3.4207 -- 123 2670 0.2804 0.3081 -- 92.0
X Ray Diffraction 3.4207 3.5129 -- 134 2697 0.2782 0.3091 -- 93.0
X Ray Diffraction 3.5129 3.616 -- 139 2745 0.2576 0.3033 -- 96.0
X Ray Diffraction 3.616 3.7323 -- 162 2787 0.2568 0.2877 -- 97.0
X Ray Diffraction 3.7323 3.8652 -- 150 2823 0.2484 0.2488 -- 97.0
X Ray Diffraction 3.8652 4.0192 -- 137 2787 0.2452 0.2772 -- 97.0
X Ray Diffraction 4.0192 4.2013 -- 173 2737 0.234 0.2546 -- 97.0
X Ray Diffraction 4.2013 4.4215 -- 154 2915 0.2247 0.2494 -- 99.0
X Ray Diffraction 4.4215 4.6966 -- 151 2788 0.205 0.2543 -- 98.0
X Ray Diffraction 4.6966 5.0562 -- 148 2862 0.2196 0.2618 -- 99.0
X Ray Diffraction 5.0562 5.5594 -- 180 2826 0.2089 0.2304 -- 99.0
X Ray Diffraction 5.5594 6.3512 -- 172 2821 0.239 0.2647 -- 99.0
X Ray Diffraction 6.3512 7.9542 -- 140 2883 0.2298 0.2602 -- 100.0
X Ray Diffraction 7.9542 24.188 -- 150 2844 0.1996 0.194 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.17
Anisotropic B[1][1] -5.51
Anisotropic B[1][2] 2.924
Anisotropic B[1][3] -2.521
Anisotropic B[2][2] 0.618
Anisotropic B[2][3] 17.083
Anisotropic B[3][3] 4.893
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.066
f_dihedral_angle_d 19.606
f_angle_d 0.971
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22867
Nucleic Acid Atoms 0
Heterogen Atoms 442
Solvent Atoms 317

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.5_2) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE: 1.5_2) refinement
PHASER model building
MAR345dtb data collection