X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 50 mM Tris, 1.9 M cesium chloride, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.8 α = 90
b = 92.8 β = 90
c = 130.1 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Collimating Mirror 2010-06-25
Diffraction Radiation
Monochromator Protocol
Double Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.45 50 99.5 -- 0.053 -- 5.8 58688 58688 -- -- --
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)
1.45 1.48 99.1 -- 0.0363 4.6 5.7 2866

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 1.45 40.184 -- 0.0 59481 56621 2860 95.86 0.1242 0.1242 0.1227 0.153 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 1.4501 1.4751 -- 126 2305 0.1503 0.1839 -- 84.0
X Ray Diffraction 1.4751 1.5019 -- 140 2479 0.1478 0.1876 -- 90.0
X Ray Diffraction 1.5019 1.5308 -- 110 2532 0.1353 0.1775 -- 92.0
X Ray Diffraction 1.5308 1.5621 -- 136 2563 0.1232 0.1946 -- 93.0
X Ray Diffraction 1.5621 1.596 -- 126 2625 0.1107 0.1491 -- 95.0
X Ray Diffraction 1.596 1.6332 -- 158 2569 0.1038 0.1556 -- 94.0
X Ray Diffraction 1.6332 1.674 -- 147 2621 0.0965 0.1479 -- 95.0
X Ray Diffraction 1.674 1.7193 -- 129 2675 0.0968 0.145 -- 96.0
X Ray Diffraction 1.7193 1.7698 -- 131 2668 0.0937 0.1169 -- 96.0
X Ray Diffraction 1.7698 1.827 -- 147 2693 0.0945 0.1405 -- 97.0
X Ray Diffraction 1.827 1.8923 -- 145 2677 0.0999 0.1334 -- 96.0
X Ray Diffraction 1.8923 1.968 -- 139 2710 0.1048 0.1556 -- 98.0
X Ray Diffraction 1.968 2.0576 -- 131 2762 0.1133 0.1535 -- 98.0
X Ray Diffraction 2.0576 2.1661 -- 154 2777 0.1132 0.1443 -- 99.0
X Ray Diffraction 2.1661 2.3018 -- 168 2746 0.1131 0.1532 -- 99.0
X Ray Diffraction 2.3018 2.4795 -- 151 2799 0.1154 0.1322 -- 99.0
X Ray Diffraction 2.4795 2.7289 -- 151 2815 0.1252 0.1463 -- 99.0
X Ray Diffraction 2.7289 3.1237 -- 142 2844 0.1361 0.1674 -- 99.0
X Ray Diffraction 3.1237 3.935 -- 168 2885 0.1294 0.1537 -- 100.0
X Ray Diffraction 3.935 40.199 -- 161 3016 0.153 0.1615 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.0657
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.0657
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.1315
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.073
f_dihedral_angle_d 14.785
f_angle_d 1.047
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2424
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 446

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
MAR345dtb data collection