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 = 92.6 α = 90
b = 92.6 β = 90
c = 131 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
1.28 50 97.3 -- 0.052 -- 5.7 83375 83375 -- -- --
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)
1.28 1.3 95.4 -- 0.326 5.3 5.7 4026

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 1.28 22.797 -- 0.0 85060 80965 4095 94.71 0.1065 0.1065 0.1055 0.1271 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 1.28 1.2951 -- 145 2427 0.1402 0.175 -- 89.0
X Ray Diffraction 1.2951 1.3108 -- 128 2436 0.1338 0.1768 -- 88.0
X Ray Diffraction 1.3108 1.3274 -- 143 2480 0.1207 0.1469 -- 91.0
X Ray Diffraction 1.3274 1.3449 -- 132 2490 0.1144 0.13 -- 90.0
X Ray Diffraction 1.3449 1.3633 -- 147 2487 0.1069 0.1267 -- 90.0
X Ray Diffraction 1.3633 1.3828 -- 128 2533 0.0945 0.1243 -- 91.0
X Ray Diffraction 1.3828 1.4034 -- 127 2521 0.1016 0.1239 -- 92.0
X Ray Diffraction 1.4034 1.4254 -- 117 2532 0.0944 0.1405 -- 91.0
X Ray Diffraction 1.4254 1.4487 -- 123 2566 0.0898 0.1364 -- 92.0
X Ray Diffraction 1.4487 1.4737 -- 141 2550 0.0878 0.1014 -- 93.0
X Ray Diffraction 1.4737 1.5005 -- 147 2600 0.084 0.128 -- 94.0
X Ray Diffraction 1.5005 1.5294 -- 139 2567 0.0853 0.1232 -- 94.0
X Ray Diffraction 1.5294 1.5606 -- 130 2655 0.0785 0.1205 -- 94.0
X Ray Diffraction 1.5606 1.5945 -- 135 2604 0.0775 0.1128 -- 95.0
X Ray Diffraction 1.5945 1.6316 -- 144 2638 0.0785 0.1042 -- 95.0
X Ray Diffraction 1.6316 1.6724 -- 106 2683 0.0826 0.1167 -- 96.0
X Ray Diffraction 1.6724 1.7176 -- 125 2703 0.0865 0.1183 -- 96.0
X Ray Diffraction 1.7176 1.7681 -- 151 2659 0.085 0.1099 -- 96.0
X Ray Diffraction 1.7681 1.8251 -- 147 2666 0.0822 0.1181 -- 97.0
X Ray Diffraction 1.8251 1.8903 -- 146 2730 0.0863 0.0964 -- 96.0
X Ray Diffraction 1.8903 1.966 -- 150 2699 0.0896 0.1127 -- 97.0
X Ray Diffraction 1.966 2.0554 -- 149 2745 0.0952 0.1146 -- 98.0
X Ray Diffraction 2.0554 2.1637 -- 164 2746 0.0915 0.1067 -- 98.0
X Ray Diffraction 2.1637 2.2991 -- 172 2739 0.0974 0.1164 -- 98.0
X Ray Diffraction 2.2991 2.4764 -- 158 2761 0.1088 0.1333 -- 98.0
X Ray Diffraction 2.4764 2.7253 -- 145 2842 0.1152 0.1543 -- 99.0
X Ray Diffraction 2.7253 3.1188 -- 146 2835 0.1143 0.1284 -- 99.0
X Ray Diffraction 3.1188 3.9261 -- 146 2918 0.1218 0.1394 -- 100.0
X Ray Diffraction 3.9261 22.8004 -- 164 3058 0.1469 0.1447 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.4496
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.4496
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.8992
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.084
f_dihedral_angle_d 15.328
f_angle_d 1.318
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2432
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 499

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