X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 300.0
Details 0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 184.52 α = 90
b = 203.87 β = 90
c = 307.87 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2012-11-12
Diffraction Radiation
Monochromator Protocol
Horizontal focusing asymmetric cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.976 CHESS A1

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
3.75 30 90.6 -- -- -- 4.2 -- 103271 -- -- --
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)
3.75 3.81 59.3 -- -- 1.4 2.0 --

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 3.85 29.966 -- 1.35 -- 101755 5085 92.44 -- 0.2667 0.2638 0.3208 --
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 3.85 3.8937 -- 133 2425 0.426 0.4227 -- 71.0
X Ray Diffraction 3.8937 3.9394 -- 132 2446 0.4104 0.3944 -- 71.0
X Ray Diffraction 3.9394 3.9873 -- 136 2589 0.3775 0.43 -- 75.0
X Ray Diffraction 3.9873 4.0377 -- 141 2715 0.3611 0.3953 -- 79.0
X Ray Diffraction 4.0377 4.0907 -- 152 2810 0.3506 0.3995 -- 81.0
X Ray Diffraction 4.0907 4.1466 -- 158 2881 0.3436 0.3975 -- 84.0
X Ray Diffraction 4.1466 4.2056 -- 149 2959 0.3487 0.3816 -- 85.0
X Ray Diffraction 4.2056 4.2682 -- 154 3042 0.3354 0.355 -- 88.0
X Ray Diffraction 4.2682 4.3347 -- 164 3109 0.3409 0.397 -- 90.0
X Ray Diffraction 4.3347 4.4056 -- 164 3185 0.3382 0.4011 -- 91.0
X Ray Diffraction 4.4056 4.4813 -- 175 3208 0.3117 0.3619 -- 94.0
X Ray Diffraction 4.4813 4.5625 -- 175 3269 0.3037 0.3528 -- 94.0
X Ray Diffraction 4.5625 4.65 -- 173 3317 0.3036 0.3529 -- 96.0
X Ray Diffraction 4.65 4.7445 -- 175 3353 0.2941 0.3106 -- 96.0
X Ray Diffraction 4.7445 4.8473 -- 176 3356 0.291 0.3668 -- 97.0
X Ray Diffraction 4.8473 4.9595 -- 177 3370 0.2848 0.3698 -- 97.0
X Ray Diffraction 4.9595 5.083 -- 176 3356 0.2764 0.3435 -- 97.0
X Ray Diffraction 5.083 5.2197 -- 181 3447 0.2779 0.3774 -- 98.0
X Ray Diffraction 5.2197 5.3725 -- 179 3417 0.2772 0.3372 -- 98.0
X Ray Diffraction 5.3725 5.5448 -- 182 3400 0.2754 0.3548 -- 98.0
X Ray Diffraction 5.5448 5.7417 -- 182 3436 0.2561 0.3639 -- 99.0
X Ray Diffraction 5.7417 5.9699 -- 182 3463 0.259 0.3726 -- 99.0
X Ray Diffraction 5.9699 6.2392 -- 180 3446 0.2589 0.3347 -- 99.0
X Ray Diffraction 6.2392 6.5649 -- 180 3462 0.233 0.322 -- 99.0
X Ray Diffraction 6.5649 6.9714 -- 183 3471 0.2331 0.3127 -- 99.0
X Ray Diffraction 6.9714 7.5018 -- 183 3489 0.2258 0.3086 -- 99.0
X Ray Diffraction 7.5018 8.2425 -- 184 3503 0.2106 0.2848 -- 99.0
X Ray Diffraction 8.2425 9.4028 -- 183 3524 0.2019 0.2614 -- 99.0
X Ray Diffraction 9.4028 11.7272 -- 185 3539 0.192 0.2352 -- 99.0
X Ray Diffraction 11.7272 29.9672 -- 191 3683 0.2452 0.2667 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.026
f_dihedral_angle_d 12.72
f_angle_d 0.649
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 56075
Nucleic Acid Atoms 0
Heterogen Atoms 124
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.2_1309) Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
PHENIX version: (phenix.refine: 1.8.2_1309) model building
HKL-2000 data collection